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Parsing the Nucleic Acids Research molecular biology online database collection
[
{
"name": "BioSample",
"url": "http://www.ebi.ac.uk/biosamples",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1458",
"desc": "Biological samples used as sources of sequence, structure or expression data",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D50",
"email": "parkinson@ebi.ac.uk"
},
{
"name": "DDBJ - DNA Data Bank of Japan",
"url": "http://www.ddbj.nig.ac.jp/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1",
"desc": "As a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), DDBJ (http://www.ddbj.nig.ac.jp) has steadily collected, annotated, released and exchanged the original DNA sequence data, which, for example, is shown by a growth curve of the data submissions in the past years (visit http://www.ddbj.nig.ac.jp/images/breakdown_stats/percentage-e.gif). However, the current situation of data submissions is dramatically changing due to the emergence of ultra-high speed or the 2nd generation sequencers (2GS) such as 454 (by 454 Life Sciences), Solexa (by Illumina, Inc.), SOLiD (by Applied Biosystems) and Helicos (by Heliscope). With these machines the whole human genome could now be sequenced at one-thousandth or less speed of the first cases in 2001 (1, 2). Recently, two reports announced that the whole genome was sequenced for two well-known persons (3, 4), which was perhaps the beginning of personal genomics. Also known is the 1000 human genomes project that is underway in USA, Europe and China to obtain a complete and detailed catalogue of genetic variations of humans (http://www.1000genomes.org/page.php). Those activities warn us that the above growth curve will steepen drastically. At present INSDC have released about 100 billion bases in total. This is the outcome of the collaboration among the three member banks for more than 20 years. However, this number will easily be surpassed when the 1000 human genomes project is completed and the result is submitted to INSDC in a few years, or even before that. To cope with those activities INSDC collaborators discussed in 2008 the attitude towards handling mass submissions produced by 2GS. The common fear among the collaborators was limited computer storages that will sooner or later be filled with continuously coming mass submissions. Nevertheless, the collaborators agreed to collect, distribute and exchange mass data of transcriptomes such as trace archives and short reads, upon the condition that the sequences are assembled. DDBJ has also started to accept and release such mass sequence data.",
"ref": "1. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W. et al. (2001) Initial sequencing and analysis of the human genome, Nature, 409, 860-921\n2. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A., Holt, R.A. et al. (2001) The sequence of the human genome, Science, 291, 1304-1351\n3. Wheeler, D.A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He W., Chen, Y.-J., Makhijani, V., Roth, G.T. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing, Nature, 452, 872-876\n4. Levy, S., Sutton, G., Ng, P.C., Feuk, L., Halpern, A.L., Walenz, B.P., Axelrod, N., Huang, J., Kirkness, E.F., Denisov, G. et al. (2008) The diploid genome sequence of an individual human, PLoS Biology, 5, 2113-2144",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D44",
"email": "ytateno@genes.nig.ac.jp"
},
{
"name": "EBI patent sequences",
"url": "http://www.ebi.ac.uk/patentdata/nr/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1340",
"desc": "Non-redundant databases of patent DNA and protein sequences",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D52",
"email": "http://www.ebi.ac.uk/support/index.php?query=PATENTDATA"
},
{
"name": "European Genome-phenome Archive (EGA)",
"url": "http://www.ebi.ac.uk/ega/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1568",
"desc": "The European Genome–phenome Archive (EGA) is a permanent repository for all types of potentially identifiable genetic and phenotypic data from biomedical research projects. The EGA contains data collected from individuals who have given consent for its use in research, but not for open public distribution. The resource accepts raw data from sequencing, genotyping, transcriptome or epigenetics experiments using next-generation sequencing platforms or array- based technologies. The service can also be used to archive any processed data, such as the locations of individual variations (e.g. SNPs) from the raw data or summary statistics from a particular project. The samples can be associated with phenotype data that have been consented for use in research. The EGA supports pre-publication data release in accordance with the Toronto agreement. The EGA provides secure access to restricted data for authorised researchers and clinicians. In all cases, data access decisions are made by the appropriate DAC and not by the EGA. Links to contact the relevant DAC are provided on each EGA study page. Approved users are issued with a personal EGA account associated with the relevant permissions. A data access agreement made between the DAC and the applicant dictates how data can be used, stored or transferred once it is downloaded from our system.",
"ref": null,
"absurl": "",
"email": "ega-helpdesk@ebi.ac.uk"
},
{
"name": "European Nucleotide Archive",
"url": "http://www.ebi.ac.uk/ena/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/2",
"desc": "The European Nucleotide Archive provides a comprehensive repository for public nucleotide sequence data, attracting external users from a multitude of research disciplines and serving as underlying data infrastructure for services such as Ensembl, UniProt and ArrayExpress. The foundation for the ENA was the EMBL Data Library, which was established in EMBL Heidelberg in the early 1980s. While this component continues to be operated to this day, the mandate of the ENA has expanded enormously as sequencing technology has advanced and the breadth of applications to which sequencing can now be applied has grown. In recent years, for example, we have launched the Sequence Read Archive (for raw data from next generation sequencing platforms) and have taken responsibility for the operation of the existing European Trace Archive (for raw capillary sequence data), which was previously operated by the Wellcome Trust Sanger Institute.\nBroadly, ENA captures and presents the whole scale of sequencing information from raw data, through assembly and mapping information that relates very fragmented raw sequence reads into contigs and higher order structures, through to high-level interpretations of the function of parts of nucleic acid molecules, in the form of functional annotation. The ENA achieves comprehensive coverage through partnership with the other global bioinformatics service providers, namely NCBI in the US and DDBJ in Japan. The longest running ENA collaboration, the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org/), has been underway for over a quarter of a century and now serves as a model for data sharing in the life sciences.",
"ref": "Kulikova, T., Aldebert, P., Althorpe, N., Baker, W., Bates, K., Browne, P., Van den Broek, A., Cochrane, G., Duggan, K., Eberhardt, R., Faruque, N., Garcia-Pastor, M., Harte, N., Kanz, C., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., Mancuso, R., McHale, M., Nardone, F., Silventoinen, V., Stoehr, P., Stoesser, G., Tuli, M.A., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W. and Apweiler, R. (2004) The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 32, D27-D30.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D18",
"email": "datasubs@ebi.ac.uk"
},
{
"name": "GenBank<sup>®</sup>",
"url": "http://www.ncbi.nlm.nih.gov/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/3",
"desc": "GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 300 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage using the link provided.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D32",
"email": "sayers@ncbi.nlm.nih.gov"
},
{
"name": "NCBI BioSample/BioProject",
"url": "http://www.ncbi.nlm.nih.gov/biosample",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1457",
"desc": "BioProject and BioSample databases at NCBI",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D57",
"email": null
},
{
"name": "neXtProt",
"url": "http://www.nextprot.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1459",
"desc": "A knowledge for human proteins",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D76",
"email": null
},
{
"name": "The Sequence Read Archive (SRA)",
"url": "http://www.ncbi.nlm.nih.gov/sra",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1456",
"desc": "Sequence Read Archive",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D54",
"email": null
},
{
"name": "ACLAME - A Classification of Mobile genetic Elements",
"url": "http://aclame.ulb.ac.be/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/403",
"desc": "A classification of genetic mobile elements",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D57",
"email": null
},
{
"name": "AREsite",
"url": "http://rna.tbi.univie.ac.at/AREsite",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1395",
"desc": "AU-rich elements in vertebrate mRNA UTR sequences",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D66",
"email": "rna@tbi.univie.ac.at"
},
{
"name": "Ciliate IES-MDS database",
"url": "http://oxytricha.princeton.edu/dimorphism/database.htm",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/649",
"desc": "Macro- and micronuclear genes in spirotrichous ciliates",
"ref": null,
"absurl": "",
"email": null
},
{
"name": "CORG - A database for COmparative Regulatory Genomics",
"url": "http://corg.molgen.mpg.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/337",
"desc": "Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG - 'COmparative Regulatory Genomics' - database. The data were computed based on statistically significant local suboptimal alignments of 15Kb regions upstream of the translation start sites of, currently, 10,793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service (http://corg.molgen.mpg.de) for query and interactive visualization of the conserved blocks and their annotation.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D32",
"email": "christoph.dieterich@molgen.mpg.de"
},
{
"name": "CUTG - Codon Usage Tabulated from GenBank",
"url": "http://www.kazusa.or.jp/codon/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/30",
"desc": "Codon usage tables",
"ref": "Nakamura, Y., Gojobori, T. and Ikemura, T. (2000). Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucl. Acids Res. 28, 292.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/28/1/292",
"email": "ynakamu@kazusa.or.jp"
},
{
"name": "Dfam",
"url": "http://dfam.janelia.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1585",
"desc": "We present a database of repetitive DNA elements, called Dfam\n(http://dfam.janelia.org). Many genomes contain a large fraction of\nrepetitive DNA, much of which is made up of remnants of transposable\nelements (TEs). Accurate annotation of TEs enables research into their\nbiology and can shed light on the evolutionary processes that shape\ngenomes. Identification and masking of TEs can also greatly simplify\nmany downstream genome annotation and sequence analysis tasks. The\ncommonly-used TE annotation tools RepeatMasker and Censor depend on\nsequence homology search tools such as cross_match and BLAST variants,\nas well as Repbase, a collection of known TE families each represented\nby a single consensus sequence. Dfam contains entries corresponding to\nall Repbase TE entries for which instances have been found in the\nhuman genome. Each Dfam entry is represented by a profile hidden\nMarkov model (HMM), built from alignments generated using RepeatMasker\nand Repbase. When used in conjunction with the HMM search tool nhmmer,\nDfam produces a 2.9% increase in coverage over consensus-sequence\nsearch methods on a large human benchmark, while maintaining low false\ndiscovery rates, and coverage of the full human genome is 54.5%. The\nwebsite provides a collection of tools and data views to support\nimproved TE curation and annotation efforts. Dfam is also available\nfor download in flat file format or in the form of MySQL table dumps.",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1265",
"email": "finnr@janelia.hhmi.org"
},
{
"name": "DiProDB",
"url": "http://diprodb.fli-leibniz.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1191",
"desc": "Database for dinucleotide properties",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D37",
"email": null
},
{
"name": "DoriC",
"url": "http://tubic.tju.edu.cn/doric5.0/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1664",
"desc": "DoriC regions in bacterial and archaeal genomes",
"ref": "1. Gao F, Zhang C.T. DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 2007 23(14):1866-7 - doi: 10.1093/bioinformatics/btm255",
"absurl": "http://dx.doi.org/10.1093/nar/gks990",
"email": "ctzhang@tju.edu.cn"
},
{
"name": "ECRbase",
"url": "http://ecrbase.dcode.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1157",
"desc": "Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and Fugu genomes. It is freely accessible at http://ecrbase.dcode.org",
"ref": "G.G. Loots and I. Ovcharenko, ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes, Bioinformatics, 23(1):122-4 (2007)",
"absurl": "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/1/122",
"email": "ovcharei@ncbi.nlm.nih.gov"
},
{
"name": "FREP",
"url": "http://facts.gsc.riken.go.jp/FREP/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/468",
"desc": "Functional repeats in mouse cDNAs",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D471",
"email": null
},
{
"name": "Genetic Codes",
"url": "http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/480",
"desc": "To ensure that the translation for each coding sequence (CDS) present in GenBank records is correct, NCBI maintains the list of genetic codes for each organism and record (shown as a /transl_table qualifier on the CDS in the flat files). The following genetic codes are described:- The Standard Code- The Vertebrate Mitochondrial Code- The Yeast Mitochondrial Code- The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code- The Invertebrate Mitochondrial Code- The Ciliate, Dasycladacean and Hexamita Nuclear Code- The Echinoderm and Flatworm Mitochondrial Code- The Euplotid Nuclear Code- The Bacterial and Plant Plastid Code- The Alternative Yeast Nuclear Code- The Ascidian Mitochondrial Code- The Alternative Flatworm Mitochondrial Code- Blepharisma Nuclear Code- Chlorophycean Mitochondrial Code- Trematode Mitochondrial Code- Scenedesmus Obliquus Mitochondrial Code- Thraustochytrium Mitochondrial Code",
"ref": null,
"absurl": "",
"email": "info@ncbi.nlm.nih.gov"
},
{
"name": "GISSD",
"url": "http://www.rna.whu.edu.cn/gissd/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1079",
"desc": "Group I Intron Sequence and Structure Database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D31",
"email": "yizhang@whu.edu.cn"
},
{
"name": "GyDB",
"url": "http://gydb.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1083",
"desc": "Gypsy database of mobile genetic elements",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D38",
"email": "carlos.llorens@uv.es"
},
{
"name": "HumHot",
"url": "http://www.jncasr.ac.in/humhot/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/825",
"desc": "HUMHOT is a web based database of human meiotic recombination hot spot DNA sequences. The database includes the hot spot sequences (",
"ref": null,
"absurl": null,
"email": "mrsrao@jncasr.ac.in"
},
{
"name": "InSatDb",
"url": "http://www.cdfd.org.in/insatdb/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/932",
"desc": "InSatDb, unlike many other microsatellite databases that cater largely to the needs of microsatellites as markers, presents an interactive interface to query information regarding microsatellite characteristics per se of five fully sequenced insect genomes (fruit-fly, honeybee, malarial mosquito, red-flour beetle and silkworm). InSatDb allows users to obtain microsatellites annotated with size (in bp and repeat units); genomic location (exon, intron, up-stream or transposon); nature (perfect or imperfect); and sequence composition (repeat motif and GC%). One can access microsatellite cluster (compound repeats) information, and a list of microsatellites with conserved flanking sequences (microsatellite family or paralogs). InSatDb is complete with the insects information, web links to find details, methodology and a tutorial. A separate Analysis section illustrates the comparative genomic analysis that can be carried out using the InSatDb output.",
"ref": "1. Archak S, Meduri E, Sravana Kumar P, Nagaraju J. (2007) InSatDb: A microsatellite database of fully sequenced insect genomes. Nucleic Acids Res. 35 (Database issue): in press.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D36",
"email": "jnagaraju@cdfd.org.in"
},
{
"name": "Isfinder",
"url": "http://www-is.biotoul.fr/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/832",
"desc": "ISfinder (http://www-is.biotoul.fr) is a dedicated database for bacterial Insertion Sequences (IS). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for IS sequences. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on Insertion Sequences and transposons in general. On-line tools are gradually being added. At present an on-line BLAST facility against the entire bank is available. Additional features will include alignment capability, PSI-BLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D32",
"email": "Michael.Chandler@ibcg.biotoul.fr"
},
{
"name": "Islander",
"url": "http://www.indiana.edu/~islander/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/512",
"desc": "Pathogenicity islands and prophages in bacterial genomes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D55",
"email": null
},
{
"name": "L1Base",
"url": "http://line1.molgen.mpg.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/697",
"desc": "Functional annotation and prediction of LINE-1 elements",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D498",
"email": null
},
{
"name": "MethDB",
"url": "http://www.methdb.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/19",
"desc": "Methylation of cytosine in the 5 position of the pyrimidine ring is a major modification of the DNA in most organisms. In eucaryotes, the distribution and number of 5-methylcytosines (5mC) along the DNA is heritable but can also change with the developmental state of the cell and as a response to modifications of the environment. DNA methylation has a number of epigenetic functions, but the scientific interest has recently focused on the gene silencing effect methylation can have in eucaryotic cells. In particular, the discovery of changes of the methylation level during cancer development has increased the interest in this field. It was also brought to light that of nutrition and drugs can influence DNA methylation patterns. We have established MethDB a public database for DNA methylation (http://www.methdb.de). This constantly growing data base has become a key resource in the field of DNA methylation research. The database contains currently methylation patterns, profiles and total methylation content data for 46 species, 160 tissues and 72 phenotypes coming from a total of 6667 experiments (as of 4/9/2002). These data can be conviniently searched and represented in different ways. Recently, we have included an on-line submission tool that permits the scientific public to directly enter data into MethDB.",
"ref": "1. Grunau C, Schattevoy R, Mache N, Rosenthal A. MethTools--a toolbox to visualize and analyze DNA methylation data. Nucleic Acids Res. 2000 Mar 1;28(5):1053-8.2. Grunau C, Renault E, Rosenthal A, Roizes G. MethDB--a public database for DNA methylation data. Nucleic Acids Res. 2001 Jan 1;29(1):270-4.3. Grunau C, Renault E, Roizes G. DNA Methylation Database 'MethDB': a User Guide. J Nutr. 2002 Aug;132(8):2435S-9S.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/29/1/270",
"email": "cgrunau@igh.cnrs.fr"
},
{
"name": "MICdb - Database of Prokaryotic Microsatellites",
"url": "http://micas.cdfd.org.in:8080/MIC/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/343",
"desc": "The MICdb (Microsatellites database) (http://www.cdfd.org.in/micas) is a comprehensive relational database of non-redundant microsatellites extracted from fully sequenced genomes. The current version (2.0) of the database is an enhanced and upgraded version compiled from 287 viral genomes as well as 129 prokaryotic genomes belonging to different phylogenetic groups and is loaded with tools and textual information so as to provide insights into structural and functional aspects of microsatellites. This database has been linked to MICAS2.0, the Web-based Microsatellite Analysis Server. MICAS provides an user-friendly front-end to systematically extract data on microsatellite tracts from hosted genomes. The database contains the following information pertaining to the microsatellites: The regions (coding/non-coding) containing microsatellite tracts, the frequencies of their occurrences, the size and the number of repeating motifs and the sequences of the tracts. Users are facilitated to query the database for details of microsatellite locations with respect to the protein coding/non-coding regions. Protein coding regions after translation are annotated with secondary structural information and positions of microsatellite tracts are shown in order to provide an insight into the possible structural changes due to microsatellite polymorphism. In the case of microsatellites occurring in the non-coding regions graphical illustrations are provided to show relative position of the microsatellite tracts with respect to the upstream and downstream coding regions. This will help in investigations on possible regulatory roles of microsatellites occurring close to protein coding regions (upstream or downstream). Sufficient textual information has been provided to help user navigation through the database and links to GenBank and Swissprot are provided to enhance information content pertaining to microsatellites. An interface to Autoprimer, a primer design program, has been provided to every microsatellite tract to compute suitable primers for PCR.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/31/1/106",
"email": "han@cdfd.org.in"
},
{
"name": "NGSmethDB",
"url": "http://bioinfo2.ugr.es/meth/NGSmethDB.php",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1321",
"absurl": null,
"email": null
},
{
"name": "NPRD - Nucleosome Positioning Region Database",
"url": "http://srs6.bionet.nsc.ru/srs6/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/707",
"desc": "Nucleosome positioning region database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D67",
"email": null
},
{
"name": "OriDB - The DNA Replication Origin Database",
"url": "http://www.oridb.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/931",
"desc": "OriDB provides a web-based catalogue of confirmed and predicted DNA replication origin sites. At present this is limited to budding yeast (S. cerevisiae). Each proposed or confirmed origin site appears as a record in OriDB, with each record comprising seven pages. These pages provide, in text and graphical formats, the following information: genomic location and chromosome context of the origin site; time of origin replication; DNA sequence of proposed or experimentally confirmed origin elements; free energy required to open the DNA duplex (stress-induced DNA duplex destabilization or SIDD); and phylogenetic conservation of sequence elements. In addition, OriDB encourages community submission of additional information for each origin site through a User Notes facility. Origin sites are linked to several external resources, including the Saccharomyces Genome Database (SGD) and relevant publications at PubMed. Finally, a Chromosome Viewer utility allows users to interactively generate graphical representations of DNA replication data genome-wide. OriDB is accessible at http://www.oridb.org/.",
"ref": "1. Nieduszynski CA, Hiraga S, Ak P, Benham CJ, Donaldson AD (2007) OriDB: a DNA Replication Origin Database. Nucleic Acids Res. 35: in press.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D682",
"email": "conrad@oridb.org"
},
{
"name": "PANDIT",
"url": "http://www.ebi.ac.uk/goldman-srv/pandit/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/608",
"desc": "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains the seed protein sequence alignments from the Pfam-A (curated families) database; nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as 'templates'; protein sequence alignments restricted to the family members for which nucleotide sequences are available; and inferred phylogenetic trees for each alignment.",
"ref": "",
"absurl": null,
"email": "pandit@ebi.ac.uk"
},
{
"name": "Patome",
"url": "http://www.patome.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/933",
"desc": "Patome contains biological sequence data disclosed in patents and published applications, as well as their analysis information. The analysis is divided into two steps. The first is an annotation step in which the disclosed sequences were annotated with RefSeq database. The second is an association step where the sequences were linked to Entrez Gene, OMIM, and GO databases, and their results were saved as a gene-patent table. Patome is available at http://www.patome.org/; the information is updated bimonthly.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D47",
"email": "bulee@kribb.re.kr"
},
{
"name": "Plant repeat database",
"url": "http://plantrepeats.plantbiology.msu.edu/index.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/588",
"desc": "Repetitive sequences in plant genomes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D360",
"email": null
},
{
"name": "PolymiRTS",
"url": "http://compbio.uthsc.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/958",
"desc": "Polymorphism in microRNA Target Site (PolymiRTS) database is a collection of naturally occurring DNA variations in putative microRNA target sites. PolymiRTSs may affect gene expression and cause variations in complex phenotypes. The database integrates sequence polymorphism, phenotype and expression microarray data, and characterizes PolymiRTSs as potential candidates responsible for the QTL (quantitative trait locus) effects. It is a resource for studying PolymiRTSs and their implications in phenotypic variations.",
"ref": "1. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams R, Cui Y. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits.Nucleic Acids Research. 35: in press.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D86",
"email": "ycui2@utmem.edu"
},
{
"name": "PseudoGene",
"url": "http://www.pseudogene.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1007",
"desc": "A compilation of published pseudogene annotations covering a wife range of both eukaryote and prokaryote genomes. The database is also divided into searchable subsets of pseudogenes sharing characteristics of interest (e.g. all expressed pseudogenes or pseudogenes found by a particular identification method), and provides the capacity to create layered unions of these sets based on user-specified set priorities.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D55",
"email": "Mark.Gerstein@yale.edu"
},
{
"name": "RECODE",
"url": "http://recode.genetics.utah.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/21",
"desc": "The RECODE database is a source for the accumulating knowledge of 'programmed' translational recoding events taken from the scientific literature and personal communications. The database deals with programmed ribosomal frameshifting, codon redefinition and translational bypass occurring in a variety of organisms. The entries for each event include the sequences of the corresponding genes, their encoded proteins for both the normal and alternate decoding, the types of the recoding events involved, and factors such as cis-elements that influence recoding. The Database is freely available at http://recode.genetics.utah.edu/.",
"ref": "Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV. (2010) Recode-2: new design, new search tools, and many more genes. Nucleic Acids Res. 2010 Jan;38(Database issue):D69-74.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/31/1/87",
"email": "baranov@howard.genetics.utah.edu"
},
{
"name": "RefSeq",
"url": "http://www.ncbi.nlm.nih.gov/RefSeq/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/391",
"desc": "The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides curated non-redundant sequence standards for genomic regions, transcripts (including splice variants), and proteins.Records are compiled using a combined approach of collaboration, automated methods, prediction, and curation and are extensively integrated with other NCBI resources facilitating navigation and discovery. RefSeq records represent the current best view of genomes and their transcript and/or protein products.",
"ref": "1. The NCBI handbook [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2002 Oct. Chapter 17, The Reference Sequence (RefSeq) Project. Available from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books2. Pruitt KD, Tatusova, T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res 2005 Jan 1;33(1):D501-D5043. Pruitt KD, Katz KS, Sicotte H, Maglott DR. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet. 2000 Jan;16(1):44-47.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D756",
"email": "info@ncbi.nlm.nih.gov"
},
{
"name": "RegTransBase",
"url": "http://regtransbase.lbl.gov/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/947",
"desc": "RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory proteins and their binding sites are already being maintained, they either focus mostly on the model organisms Escherichia coli and Bacillus subtilis or are entirely computationally derived.RegTransBase describes a large number of regulatory interactions reported in many organisms and contains the following types of experimental data:the activation or repression of transcription by an identified direct regulator, determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA (RNA), mapping or prediction of a binding site for a regulatory protein, and characterization of regulatory mutations.Currently, RegTransBase content is derived from about 3000 relevant articles describing over 7000 experiments in relation to 128 microbes. It contains data on the regulation of about 7500 genes and evidence for 6500 interactions with 650 regulators. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species.",
"ref": "Kazakov A.E., Cipriano M.J., Novichkov P.S., Minovitsky S., Vinogradov D.V., Arkin A.P., Mironov A.A., Gelfand M.S. and Dubchak I. (2007) RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res., 35: in press.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D407",
"email": "ildubchak@lbl.gov"
},
{
"name": "RetrOryza",
"url": "http://www.retroryza.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1019",
"absurl": null,
"email": null
},
{
"name": "S/MARt DB",
"url": "http://smartdb.bioinf.med.uni-goettingen.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/309",
"desc": "The nuclear organization of metaphase and interphase cells has been studied over several decades and increasing evidence supports the concept upon which the eukaryotic chromatin is organized in the form of functional independent loop domains [1; 2]. Scaffold/matrix attached regions (S/MARs) are DNA sequences that mediate the tight contact of the chromatin with the proteinaceous scaffold within the nucleus. They have shown to be necessary for chromatin loops to form [3] and they were observed at the base of chromatin loops [4]. S/MARs have also been assigned to function in gene expression. Recently it has been shown that S/MARs can serve as landing platforms for several chromatin remodeling factors and thereby influence gene expression [5]. S/MARs were also attributed a fundamental role in carcinogenesis [6].S/MARt DB is a curated database which collects information about S/MARs and nuclear proteins which are involved in the interaction of these elements with the nuclear scaffold [7]. Its wet-lab verified data are compiled predominantly from publications in peer-reviewed journals. The database equipped with tools for searching and browsing is freely accessible through WWW (http://smartdb.bioinf.med.uni-goettingen.de/) for users from non-profit organizations.The data presented as three hyperlinked files for the use via the internet come mainly from animal and plant species.S/MARt DB has been enlarged by new entries to 500 S/MAR entries in the recent release and improved further by updating of already existing entries in each of its tables. With release 2.2 the database was complemented by hyperlinks to EntrezGene and Ensembl, respectively. They serve to incorporate S/MARt DB into a European network of biological databases which is going to be build up in the context of the TEMBLOR project.",
"ref": "1. Gasser, S. M. and Laemmli, U. K. (1987) A glimpse at chromosomal order, Trends Genet. 3, 16-22.2. Heng, H. H. Q., Krawetz, S. A., Lu, W., Bremer, S., Liu, G. and Ye, C. J. (2001) Re-defining the chromatin loop domain, Cytogenet. Cell Genet.. 93, 1551-1561.3. Heng, H. H. Q., Goetze, S., Ye, C. J., Liu, G., Stevens, J. B., Bremer, S. W., Wykes, S. M., Bode, J. and Krawetz, S. A. (2004) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions, J. Cell Sci. 117, 999-1008.4. Cai, S., Han, H.-J. and Kohwi-Shigematsu, T. (2003) Tissue-specific nuclear architecture and gene expression regulated by SATB1, Nat. Genet. 34, 42-515. Yasui, D., Miyano, M., Cai, S., Varga-Weisz, P. and Kohwi-Shigematsu, T. (2002) SATB1 targets chromatin remodelling to regulate genes over long distances, Nature 419, 641-645.6. Will,K., Warnecke,G., Albrechtsen,N., Boulikas,T. and Deppert,W. (1998) High affinity MAR-DNA binding is a common property of murine and human mutant p53. J. Cell. Biochem. 69, 260-270.7. Liebich,I. Bode,J., Frisch,M. and Wingender,E. (2002) S/MARt DB: a database on scaffold/matrix attached regions. Nucleic Acids Res. 30, 372-374.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/30/1/372",
"email": "smartdb@bioinf.med.uni-goettingen.de"
},
{
"name": "SINEBase",
"url": "http://sines.eimb.ru/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1586",
"desc": "A database of short interspersed elements (SINEs)",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1263",
"email": "kramerov@genome.eimb.relarn.ru"
},
{
"name": "SNPSTR",
"url": "http://www3.imperial.ac.uk/theoreticalgenomics/data-software/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1013",
"desc": "The SNPSTR database contains the SNP-STR/microsatellite compound markers in the five model species, where sufficient SNP information exists in both of the NCBI and Ensembl databases. These species are human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), dog (Canis familiaris) and chicken (Gallus gallus).",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D71",
"email": "ino.agrafioti@imperial.ac.uk"
},
{
"name": "STRBase",
"url": "http://www.cstl.nist.gov/div831/strbase/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/47",
"desc": "Short tandem DNA repeats",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/29/1/320",
"email": "john.butler@nist.gov"
},
{
"name": "Synthetic Gene Database",
"url": "http://www.umbc.edu/codon/sgdb/index.php",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/929",
"desc": "The Synthetic Gene Database (http://www.evolvingcode.net/codon/sgdb/index.php) is a resource that has collected together sequence information on synthetic genes (i.e. genes that were designed conceptually, rather than built from an initial, physical template). Specifically it collates all such genes that have been reported in the peer-reviewed literature to date, along with associated meta-data, including details of the publication and of their expression.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D76",
"email": "freeland@umbc.edu"
},
{
"name": "TassDB",
"url": "http://www.tassdb.info/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/927",
"desc": "TassDB (TAndem Splice Site DataBase) stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. These splice events are of subtle nature since they mostly result in the insertion/deletion of a single amino acid or the substitution of one amino acid by two others. Currently, TassDB contains 114,554 tandem splice sites of eight species, 5,209 of which have EST/mRNA evidence for alternative splicing. In addition, human SNPs that affect NAGNAG acceptors are annotated. The database provides a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download large datasets. The aim of this database is to facilitate experimental studies and large-scale bioinformatics analyses of tandem splice sites.",
"ref": "",
"absurl": null,
"email": "TassDB2@tassdb.info"
},
{
"name": "TIGR Plant Transcript Assembly database",
"url": "http://plantta.tigr.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/940",
"desc": "The TIGR Plant Transcript Assemblies (TA) database (http://plantta.tigr.org) uses expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of transcript assemblies. The sequences collected include expressed Sequence Tags (ESTs) and full-length and partial cDNAs, but exclude computationally predicted gene sequences.The TA database includes all plant species for which more than 1,000 EST and cDNA sequences are publicly available. The database can be searched by species, by keyword or by sequence via BLAST.The sequences of the TAs are available for downloading.",
"ref": "1. Childs K.L., Hamilton J., Zhu W., Ly E., Cheung F., Wu H., Rabinowicz P.B., Town C.D., Buell C.R., Chan A.P. (2007) The TIGR Plant Transcript Assemblies Database.Nucleic Acids Res. 35: in press.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D846",
"email": "kchilds@tigr.org"
},
{
"name": "TranspoGene",
"url": "http://transpogene.tau.ac.il/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1142",
"desc": "Transposed elements influence on the transcriptome of seven vertebrates and invertebrates",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D47",
"email": "asaflev1@post.tau.ac.il"
},
{
"name": "TRDB",
"url": "http://tandem.bu.edu/cgi-bin/trdb/trdb.exe",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1035",
"desc": "Tandem repeats in genomic DNA",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D80",
"email": null
},
{
"name": "UCbase and miRfunc",
"url": "http://ucbase.unimore.it/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1230",
"desc": "Ultraconserved sequences (UCRs) were first described by Bejerano et al. in 2004. They are highly conserved genome regions that share 100% identity among human, mouse and rat. UCRs are 481 sequences longer than 200 bases. They are frequently located at genomic regions involved in cancer, differentially expressed in human leukemias and carcinomas. Here we present an updated version of UCbase, that includes new annotation based on hg19 Human genome, information about disorders related to the chromosome coordinates using the SNOMED classification, a query tool to search for SNPs, and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive, visual interpretation of UCR chromosomal coordinates, we have re-implemented the graph visualization feature of UCbase creating a link to UCSC genome browser. Due to the existence of new databases focused on non-coding RNAs, UCbase 2.0 does not provide microRNAs information anymore focusing only on UCRs. As a web application, UCbase 2.0 is platform independent and it is accessible at http://ucbase.unimore.it.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D41",
"email": "ucbase-help@xlabserver3.biomed.unimo.it"
},
{
"name": "UCNEbase",
"url": "http://ccg.vital-it.ch/UCNEbase/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1587",
"desc": "A database of ultraconserved non-coding elements and gene regulatory blocks",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1092",
"email": "Philipp.Bucher@epfl.ch"
},
{
"name": "UgMicroSatdb",
"url": "http://ipu.ac.in/usbt/UgMicroSatdb.htm",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1144",
"desc": "UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D53",
"email": "deansbt@yahoo.co.in"
},
{
"name": "UniVec",
"url": "http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/320",
"desc": "UniVec is a non-redundant database of sequences commonly attached to cDNA or genomic DNA during the cloning process. This database is intended to be used for screening nucleic acid sequences for vector contamination. UniVec primarily consists of the unique segments from a large number of vectors but also includes many linker, adapter and primer sequences. Redundant sub-sequences have been eliminated from the database to make searches more efficient and to simplify interpretation of the results.",
"ref": null,
"absurl": "",
"email": "info@ncbi.nlm.nih.gov"
},
{
"name": "UTRdb/UTRsite",
"url": "http://utrdb.ba.itb.cnr.it/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/252",
"desc": "The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, a specialized database of 5' and 3' untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All internet resources we implemented for retrieval and functional analysis of 5' and 3' untranslated regions of eukaryotic mRNAs are accessible at http ://bighost.area.ba.cnr.it/BIG/UTRHome/",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D75",
"email": "graziano.pesole@unimi.it"
},
{
"name": "UTRome",
"url": "http://www.utrome.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1147",
"desc": "3'UTRs and their functional elements in C. elegans",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D57",
"email": "kcg1@nyu.edu"
},
{
"name": "VectorDB",
"url": "http://downloads.yeastgenome.org/unpublished_data/vectordb/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/302",
"desc": "Data available for download from the SGD site, be aware that data dates from 1997",
"ref": null,
"absurl": "",
"email": "sgd-helpdesk@lists.stanford.edu"
},
{
"name": "VISTA Enhancer Browser",
"url": "http://enhancer.lbl.gov/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/968",
"desc": "Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo.This paucity of enhancer collections with defined activities has thus hindered computational approaches for the genome-wide prediction of enhancers and their functions.To fill this void, we utilize comparative genome analysis to identify candidate enhancer elements in the human genome coupled with the experimental determination of their in vivo enhancer activity in transgenic mice.These data are available through the VISTA Enhancer Browser (http://enhancer.lbl.gov).This growing database currently contains over 250 experimentally tested DNA fragments, of which more than 100 have been validated as tissue-specific enhancers.For each positive enhancer, we provide digital images of whole-mount embryo staining at embryonic day 11.5 and an anatomical description of the reporter gene expression pattern.Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to a particular tissue, or download entire collections of enhancers with a defined tissue specificity or conservation depth.These experimentally validated training sets are expected to provide a basis for a wide range of downstream computational and functional studies of enhancer function.",
"ref": null,
"absurl": null,
"email": "LAPennacchio@lbl.gov"
},
{
"name": "APPRIS",
"url": "http://appris.bioinfo.cnio.es/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1588",
"desc": "A system for annotating alternative splice isoforms",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1058",
"email": "mtress@cnio.es"
},
{
"name": "ARTADEdb",
"url": "http://omicspace.riken.jp/ARTADE/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/880",
"desc": "The tiling array is a powerful tool to discover the unknown transcripts that were essentially undetectable by construction of cDNA libraries or by strictly sequence-based gene predictions. Here we introduce a database named ARTADEdb containing transcriptional structures elucidated by our original statistical method ARTADE which estimates exon/intron structures of structurally unknown genes based on both tiling array data and genomic sequence data. By applying it to genome-wide tiling array data from four tissues in Arabidopsis, 14,782 transcriptional units (TUs) including 5,250 novel TUs found in the intergenic regions were registered in ARTADEdb. As 84.4% of the novel TUs were verified to be actually expressed by comparison with Arabidopsis UniGene clusters, the results are of benefit for researchers hunting for novel genes and their functions. The predicted genes were annotated with information on their expression values, significances of the expressions, nucleic- and amio-acid sequences, functionally known references, and were clustered as TUs based on their genomic positions. For the user’s convenience, the gene records are related to available mutants, full-length cDNAs, literature-based related genes, and ontologies. In the database system, the genes can be searched by specifying keywords related to the above-mentioned annotations, filtered by expression cutoffs or other criteria, and the resulting list is ranked based on various parameters. The system also supplies a primer-designing function so that promising candidate genes are quickly verified experimentally. The database is integrated in our original data-retrieval framework named GPS: Genome?Phenome Superhighway, and is accessible at http://omicspace.riken.jp/ARTADE/.",
"ref": null,
"absurl": "",
"email": "toyop@gsc.riken.jp"
},
{
"name": "ASAP II",
"url": "http://www.bioinformatics.ucla.edu/ASAP2/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/414",
"desc": "We have greatly expanded the Alternative Splicing Annotation Project (ASAP, http://www.bioinformatics.ucla.edu/ASAP) database:i) its human alternative splicing data is expanded about 3-fold over the previous ASAP database, to nearly 90,000 distinct alternative splicing events;ii) it now provides genome-wide alternative splicing analyses for 15 vertebrate, insect, and other animal species;iii) it provides comprehensive comparative genomics information for comparing alternative splicing and splice site conservation across 17 aligned genomes, based on UCSC multigenome alignments;iv) it provides an approximately 2 ~ 3 fold expansion in detection of tissue-specific alternative splicing events, and of cancer vs. normal specific alternative splicing events.We have also constructed a novel database linking orthologous exons and orthologous introns between genomes, based on multigenome alignment of 17 animal species.It can be a valuable resource for studies of gene structure evolution.",
"ref": "\n1. Lee, C., Atanelov, L., Modrek, B. and Xing, Y. (2003) ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res, 31, 101-105.\n2. Modrek, B., Resch, A., Grasso, C. and Lee, C. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res, 29, 2850-2859.\n3. Kim, P., Kim, N., Lee, Y., Kim, B., Shin, Y. and Lee, S. (2005) ECgene: genome annotation for alternative splicing. Nucleic Acids Res, 33, D75-79.\n4. Kim, N., Shin, S. and Lee, S. (2005) ECgene: genome-based EST clustering and gene modeling for alternative splicing. Genome Res, 15, 566-576.\n5. Xu, Q. and Lee, C. (2003) Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res, 31, 5635-5643.\n6. Xu, Q., Modrek, B. and Lee, C. (2002) Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res, 30, 3754-3766.\n7. Resch, A., Xing, Y., Alekseyenko, A., Modrek, B. and Lee, C. (2004) Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res, 32, 1261-1269.\n8. Roy, M., Xu, Q. and Lee, C. (2005) Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms. Nucleic Acids Res, 33, 5026-5033.\n9. Chen, F.C., Wang, S.S., Chen, C.J., Li, W.H. and Chuang, T.J. (2006) Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol, 23, 675-682.\n10. Xing, Y., Wang, Q. and Lee, C. (2006) Evolutionary divergence of exon flanks: a dissection of mutability and selection. Genetics, 173, 1787-1791.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D93",
"email": "leec@mbi.ucla.edu"
},
{
"name": "ASHESdb",
"url": "http://sege.ntu.edu.sg/wester/ashes/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/639",
"desc": "Alternatively spliced human genes by exon skipping database",
"ref": null,
"absurl": "",
"email": null
},
{
"name": "ASPicDB",
"url": "http://www.caspur.it/ASPicDB/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1397",
"desc": "Alternative Splicing Prediction DataBase",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D80",
"email": "graziano.pesole@biologia.uniba.it"
},
{
"name": "ASTD",
"url": "http://www.ebi.ac.uk/astd/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/28",
"desc": "The Alternative Splicing Database (ASD) Project aims to understand the mechanism of alternative splicing on a genome-wide scale by creating a database of alternative splice events and the resultant isoform splice patterns of genes from human, and other model species.",
"ref": null,
"absurl": null,
"email": "asd-ebi@ebi.ac.uk"
},
{
"name": "ChimerDB",
"url": "http://genome.ewha.ac.kr/ChimerDB/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/803",
"desc": "ChimerDB is a database of fusion sequences encompassing bioinformatics analysis of mRNA and EST sequences in the GenBank, manual collection of literature data and integration with other well known databases. Fusion transcripts with nonoverlapping alignments at multiple genomic loci were identified and filtered to remove cloning artifacts in cDNA library preparation. Fusion transcripts are classified into two groups - genuine chromosome translocation and fusion between neighboring genes owing to intergenic splicing. Literature data from pubmed abstracts and the fusion data from public resources (OMIM, Sanger CGP, Atlas chromosomes in cancer, and the Mitelman's breakpoint) are integrated to enhance the coverage and reliability. Currently, ChimerDB contains 1,258 fusion cases that involve 1,777 genes, 381 mRNA and 654 EST sequences. It can be accessed at http://genome.ewha.ac.kr/ChimerDB/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D21",
"email": "sanghyuk@ewha.ac.kr"
},
{
"name": "ChiTaRS",
"url": "http://chimerasrch.bioinfo.cnio.es/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1589",
"desc": "Chimeric RNAs of two or more different transcripts",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1041",
"email": "mmorgenstern@cnio.es"
},
{
"name": "DBASS5/3",
"url": "http://www.dbass.org.uk/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1308",
"desc": "Database of Aberrant Splice Sites: sequences flanking cryptic and de novo 3' and 5' splice sites",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D86",
"email": "igvo@soton.ac.uk"
},
{
"name": "ECgene",
"url": "http://genome.ewha.ac.kr/ECgene/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/667",
"desc": "Genome annotation for alternative splicing",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D99",
"email": null
},
{
"name": "EDAS - EST-Derived Alternative Splicing Database",
"url": "http://edas2.bioinf.fbb.msu.ru/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/631",
"desc": "EDAS is a database of alternative splicing derived from the anlaysis of genomic, protein, mRNA and EST data. It provides classification of elementary alternatives into main types, combined searches for specific alternative variants over tissues and disease states, curated classification of cancer-derived clone libraries by origin (cell line or primary donor tissue), a convenient user interface with in-scale and schematic representation of the alternative exon-intron structure, and a possibility to filter data by the reliability of sources.",
"ref": "1. Nurtdinov, R.N., Artamonova, I.I., Mironov, A.A., and Gelfand, M.S. (2003) Low conservation of alternative splicing patterns in the human and mouse genomes. Hum. Mol. Genet. 2003, 12: 1313-1320.2. Mironov, A.A., Novichkov, P.S., and Gelfand, M.S. (2001) Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics, 17, 13-15.3. Mironov, A.A., Fickett, J.W., and Gelfand, M.S. (1999) Frequent alternative splicing of human genes. Genome Res. 1999, 9: 1288-1293.\n4. Nurtdinov, R.N., Neverov, A.D., Favorov, A.V., Mironov, A.A., and Gelfand, M.S. (2007) Conserved and species-specific alternative splicing in mammalian genomes. BMC Evol Biol. 2007 7:249.",
"absurl": "",
"email": "gelfand@iitp.ru"
},
{
"name": "EID: Exon-Intron Database",
"url": "http://bpg.utoledo.edu/~afedorov/lab/eid.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/32",
"desc": "The Exon-Intron Database (EID), publicly available since 2000, is a flat-file, Fasta-formated collection of sequences and annotations for all exons and introns obtained from GenBank. The primary goal of EID is to offer a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. New innovations in EID have been implemented in 2005. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well.Intron-less genes are included as a special part of EID.For species with entirely sequenced genomes, species-specific databases have been generated. Currently, these species-specific sets of all introns and all exons are available for human, mouse, rat, dog, chicken, zebrafish, fruit fly, worm (C. elegans), and mouse-ear cress (A. thaliana). This list will be extended on a monthly basis in accordance with GenBank updates. EID is freely available at http://www.meduohio.edu/bioinfo/eid/.",
"ref": "1.Saxonov, S., Daizadeh, I., Fedorov, A. and Gilbert, W. (2000) EID: The Exon-Intron Database: An exhaustive database of protein-containing genes. Nucl. Acids Res., 28, 185-190.2. Fedorov, A., Stombaugh, J., Harr, M.W., Yu, S., Nasalean, L. and Shepelev, V. (2005) Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database. Nucl. Acids Res., 33, 4578-4583.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/28/1/185",
"email": "alexei.fedorov@utoledo.edu"
},
{
"name": "ExtraTrain",
"url": "http://www.era7.com/ExtraTrain/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/913",
"desc": "ExtraTrain is a new database for exploring Extragenic and Transcriptional information in prokaryotic organisms. Transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. In these processes, the regulatory signals located in DNA extragenic regions and the regulatory proteins are the key elements involved. As all extragenic spaces are putative regulatory regions, ExtraTrain covers all extragenic regions of available genomes and all regulatory proteins included in the UniProt database corresponding to bacteria and archaea. ExtraTrain provides integrated and easily manageable information for 679816 extragenic regions and for the genes delimiting each of them. ExtraTrain supplies a tool to explore extragenic regions, named Palinsight, oriented to detect and search palindromic patterns. This interactive visual tool is totally integrated in the database, allowing the search for regulatory signals in user defined sets of extragenic regions. The 26046 regulatory proteins included in ExtraTrain are classified in 16 families following the InterPro criteria. The information about regulators includes manually curated sets of references specifically associated to regulator entries.In order to achieve a sustainable and maintainable knowledge database ExtraTrain is a platform open to the contribution of knowledge by the scientific community providing a system for the incorporation of textual knowledge by the scientists. ExtraTrain database is available at http://www.era7.com/ExtraTrain/.",
"ref": null,
"absurl": "",
"email": "rtobes@era7.com"
},
{
"name": "FESD - Functional Element SNPs Database",
"url": "http://sysbio.kribb.re.kr:8080/fesd/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/669",
"desc": "Functional Element SNPs Database (FESD) categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. In the FESD, the human genic regions were divided into 10 different functional elements, such as promoter regions, CpG islands, 5’-untranslated regions (5’-UTRs), translation start sites, splice sites, coding exons, introns, translation stop sites, polyadenylation signals and 3’-UTRs, and subsequently, all the known SNPs were assigned to each functional element at their respective position. With the FESD web interface, users can select a set of SNPs in the specific functional elements and get their flanking sequences for genotyping experiments, which will help in finding mutations that contribute to the common and polygenic diseases.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D518",
"email": "yjkim8@kribb.re.kr"
},
{
"name": "FUGOID",
"url": "http://fugoid.webhost.utexas.edu/introndata/main.htm",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/782",
"desc": "Introns in organelle genomes demonstrate wide variation in both features and behavior in Nature. Three classes of organelle introns are now recognized: 1) Group I, 2) Group II, and 3) Group III which are related to Group II introns. These introns have attracted considerable attention because of two remarkable properties: 1) the ability to self-splice, 2) the ability to function as mobile elements. These properties are being explored in order to understand gene evolution and as potential tools in genetic engineering and genomic analysis",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/30/1/385",
"email": "dlherrin@utxvms.cc.utexas.edu"
},
{
"name": "GeneTack",
"url": "http://topaz.gatech.edu/GeneTack/db.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1590",
"desc": "Genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1062",
"email": "borodovsky@gatech.edu"
},
{
"name": "H-DBAS",
"url": "http://jbirc.jbic.or.jp/h-dbas/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/970",
"desc": "The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a specialized database of alternatively spliced human transcripts. In this database, each of the alternative splicing variants corresponds to a completely sequenced and carefully annotated human full-length cDNA, one of those collected for the H-Invitational human transcriptome annotation meeting. H-DBAS contains 38 664 representative alternative splicing variants in 11 744 loci, in total. The data is retrievable by various features of alternative splicing, which were annotated according to manual annotations, such as by patterns of alternative splicings, consequently invoked alternations in the encoded amino acids and affected protein motifs, GO terms, predicted subcellular localization signals and transmembrane domains. The database also records recently identified very complex patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or degenerated (multiple CDS): in all three cases, completely unrelated proteins are encoded by a single locus. By using AS Viewer, each alternative splicing event can be analyzed in the context of full-length cDNAs, enabling the user’s empirical understanding of the relation between alternative splicing event and the consequent alternations in the encoded amino acid sequences together with various kinds of affected protein motifs. H-DBAS is accessible at http://jbirc.jbic.or.jp/h-dbas/.",
"ref": "1. Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M. et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol, 2, e162.\n2. Takeda, J., Suzuki, Y., Nakao, M., Barrero, R.A., Koyanagi, K.O., Jin, L., Motono, C., Hata, H., Isogai, T., Nagai, K. et al. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res, 34, 3917-3928.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D86",
"email": "jtakeda@jbirc.aist.go.jp"
},
{
"name": "HEXEvent",
"url": "http://hertellab.mmg.uci.edu/cgi-bin/HEXEvent/HEXEventWEB.cgi",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1591",
"desc": "Human Exone Splicing Events",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks969",
"email": "khertel@uci.edu"
},
{
"name": "Hollywood",
"url": "http://hollywood.mit.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/821",
"desc": "Exon annotation database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D56",
"email": "holste@MIT.EDU"
},
{
"name": "HS<sup>3</sup>D - Homo Sapiens Splice Sites Dataset",
"url": "http://www.sci.unisannio.it/docenti/rampone/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/36",
"desc": "In the last years many computational tools for gene identification and characterization[1,2,3,4,5,6,7,8 and many others], mostly based on machine learning approaches, have been used. In the machine learning approach, a learning algorithm receives a set of training examples, each labelled as belonging to a particular class. The algorithm’s goal is to produce a classification rule for correctly assigning new examples to these classes. The success of these methods depends largely on the quality of the data sets that are used as the training set[9]. Furthermore a common data set is necessary when the prediction accuracy of different programs needs to be comparatively assessed[10,11]. The Irvine Primate Splice Junctions Dataset (UCI Machine Learning Repository http://www.ics.uci.edu/~mlearn/MLRepository.html) is a standard “de facto” in the machine learning community [12,13,14,15 and many others], but it is now very out of date and do not include sufficient material for the most learning algorithm needs. A recent and EST confirmed data set[16] has the same limitation in the data extend. More recently Burset et al.[17] developed an extensive data base, but the data do not include false splice sites (negative examples), and, specifically, proximal false splice sites. The latter data form a well known critical point of classification systems[11]. We developed a new database (HS3D - Homo Sapiens Splice Site Dataset) of Homo Sapiens Exon, Intron and Splice regions. The aim of this data set is to give standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank Primate Sequences Rel.123 (8436 entries), 697 entries of Human Nuclear DNA including a Gene with Complete CDS and with more than one exon have been selected according to assessed selection criteria[18] (file genbank_filtered.inf). 4450 exons and 3752 introns have been extracted from these entries (files exons.seq and introns.seq). Several statistics for such exons and introns (overall nucleotides, average GC content, number of exons/introns including not AGCT bases, number of exons/introns in which the annotated end is not found, exon/intron minimum length, exon/intron maximum length, exon/intron average length, exon/intron length standard deviation, number of introns in which the sequence does not start with GT, number of introns in which the sequence does not end with AG) are reported (files exons.stat and introns.stat). Then 3762 + 3762 donor and acceptor sites have been extracted as windows of 140 nucleotides around each splice site. After discarding sequences not including canonical GT–AG junctions (176 +191), including insufficient data (not enough material for a 140 nucleotide window) (590+547), and including not AGCT bases (30+32), there are 2955+2992 windows (files GT_true.seq and AG_true.seq). Information and several statistics about the splice sites extraction are reported (files GT_true.inf, AG_true.inf, GT_true.stat, and AG_true.stat). Finally, there are 287,296+348,370 windows of false splice sites, selected by searching canonical GT–AG pairs in not splicing positions. The false sites in a range+/- 60 from a true splice site are marked as proximal (files GT_false.seq, and AG_false.seq) (Related information: GT_false.inf, and AG_false.inf). HS3D is available at the Web server of the University of Sannio http://www.sci.unisannio.it/docenti/rampone/",
"ref": "1. S. Brunak, J. Engelbrecht, and S. Knudsen (1991) Prediction of the human mRNA donor and acceptor sites from the DNA Sequence, J.Mol.Biol., 220, 49- 65.2. V.V. Solovyev, A.A.Salamov, and C.B. Lawrence ( 1994) Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames. Nucleic Acids Research, 22, 5156-5163.3. J. Henderson, S. Salzberg, and K.H. Fasman ( 1997) Finding Genes in DNA with a Hidden Markov Model. J. Comput. Biol. 4(2) 127-414. N. Friedman, D. Geiger, and M. Goldszmidt (1997 ) Bayesian network classifiers. Machine Learning, 29, 131-163.5. M.Q. Zhang (1997) Identification of protein coding regions in the human genome by quadratic discriminant analysis, Proc. Natl. Acad. Sci. USA, 94, 565-568.6. A. Krogh (1998) An Introduction to Hidden Markov Models for Biological Sequences. In Computational methods in Molecular Biology, S.L. Salzberg, D.B.Searls, and S.Kasif ed.s, Elsevier, 45-63.7. S. Rampone (1998) Recognition of Splice- Junctions on DNA Sequences by BRAIN learning algorithm. Bioinformatics, 14(8), 676-684.8. D. Cai, A. Delcher, B. Kao, and S. Kasif (2000) Modelling splice sites with Bayes Networks. Bioinformatics, 16(2), 152:158.9. C.M. Bishop (1995) Neural Networks for Pattern Recognition, Oxford University Press.10. M. Burset, and R. Guigo (1996). Evaluation of gene structure prediction programs. Genomics, 34, 353-367.11. T.A. Thanaraj (2000) Positional Characterisation of False Positives from Computational Prediction of Human Splice Sites. Nucleic Acids Research, 28(3), 744-754.12. M.O. Noordewier, G.G. Towell and J.W. Shavlik, (1991) Training Knowledge-Based Neural Networks to Recognize Genes in DNA Sequences. Advances in Neural Information Processing Systems, volume 3, Morgan Kaufmann.13. G.G. Towell, J.W. Shavlik, and M.W. Craven ( 1991) Constructive Induction in Knowledge-Based Neural Networks. In Proceedings of the Eighth International Machine Learning Workshop, Morgan Kaufmann.14. G.G. Towell (1991) Symbolic Knowledge and Neural Networks: Insertion, Refinement, and Extraction. PhD Thesis, University of Wisconsin - Madison.15. G.G. Towell, and J.W. Shavlik (1992) Interpretation of Artificial Neural Networks: Mapping Knowledge-based Neural Networks into Rules . In Advances in Neural Information Processing Systems, volume 4, Morgan Kaufmann.16. T.A. Thanaraj (1999) A Clean data set of EST- confirmed Splice Sites from Homo Sapiens and Standards for Clean-up Procedures. Nucleic Acids Research, 27(13), 2627-2637.17. M. Burset, I.A. Seledtsov, and V.V. Solovyev ( 2001) SpliceDB: database of canonical and non- canonical mammalian splice sites, Nucleic Acids Research, 29(1), 255-25918. T.A. Thanaraj (1999) Standards to Create Clean Data Sets for Gene Prediction. Bioinformer, Fall ` 99, http://bioinformer.ebi.ac.uk/newsletter/archives/5/gene_prediction.html.19. P.Pollastro, S.Rampone (2002), IJMPC, 13(8), 2002.",
"absurl": "",
"email": "rampone@unisannio.it"
},
{
"name": "ProSAS",
"url": "http://services.bio.ifi.lmu.de/ProSAS/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1122",
"desc": "Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D63",
"email": "fabian.birzele@bio.ifi.lmu.de"
},
{
"name": "SpliceAid-F",
"url": "http://mi.caspur.it/SpliceAidF/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1592",
"desc": "Human splicing factors and their RNA binding sites",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks997",
"email": "graziano.pesole@biologia.uniba.it"
},
{
"name": "SpliceDB",
"url": "http://linux1.softberry.com/berry.phtml?topic=splicedb",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/46",
"desc": "Canonical and non-canonical mammalian splice sites",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/29/1/255",
"email": "solovyev@eosbiotech.com"
},
{
"name": "SpliceInfo",
"url": "http://spliceinfo.mbc.nctu.edu.tw/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/746",
"desc": "Modes of alternative splicing in human genome",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D80",
"email": null
},
{
"name": "SpliceNest",
"url": "http://splicenest.molgen.mpg.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/580",
"desc": "A tool for visualizing splicing of genes from EST data",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/30/1/299",
"email": null
},
{
"name": "Spliceosome Database",
"url": "http://spliceosomedb.ucsc.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1593",
"absurl": "http://dx.doi.org/10.1093/nar/gks999",
"email": "mjurica@ucsc.edu"
},
{
"name": "U12DB",
"url": "http://genome.crg.es/cgi-bin/u12db/u12db.cgi",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/937",
"desc": "U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12-type introns of completely sequenced eukaryotic genomes in a framework that groups orthologous introns with each other. This will aid further investigations into the evolution and mechanism of U12-dependent splicing as well as assist ongoing genome annotation efforts.Public access to the U12 Intron Database is available at http://genome.crg.es/cgi-bin/u12db/u12db.cgi.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D110",
"email": "talioto@imim.es"
},
{
"name": "uORFdb",
"url": "http://cbdm.mdc-berlin.de/tools/uorfdb/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1674",
"desc": "Upstream ORFs and their effect of translation of downstream CDSs",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D60",
"email": "aleutz@mdc-berlin.de"
},
{
"name": "Yeast Intron Database",
"url": "http://www.cse.ucsc.edu/research/compbio/yeast_introns.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/342",
"desc": "This searchable database contains information about the location, structure, and function of spliceosomal introns in the nuclear genome of Saccharomyces cerevisiae. Searches produce reports for each intron satisfying the search criteria, showing key information, including a short gene description with links to the Saccharomyces Genome Database, estimated transcription rate, special features of the intron, literature or EST verification links, intron size, splice sites and branchpoint sequences and complete sequences of the intron and flanking exons, as well as the sequence generated by splicing. Expression measurements that profile the impact of mutations on the splicing of each intron are also included in the reports. The underlying data can also be downloaded in generic formats. We enjoy hearing suggestions, corrections, and new information and can update the information easily.",
"ref": " Ares, M., Grate, L., and Pauling, M. H. (1999) A handful of intron-containing genes produce the lion’s share of yeast mRNA. RNA 5:1138-1139. Clark, T., Sugnet, C., and Ares, M. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296: 907-10.Davis, C., Grate L., Spingola, M., and Ares, M. (2000) Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucl. Acids Res. 28: 1700-1706.Grate, L., and Ares, M. (2002) Searching Yeast Intron Data at the Areslab Website. (In Guide to Yeast Genetics and Molecular and Cell Biology, Part B, C. Guthrie and G. Fink, eds) Methods Enz. 350: 380-392. Spingola, M., Grate, L., Haussler, D., and Ares, M. (1999)ÂGenome-wide bioinformatic and molecular analysis of yeast introns. RNA 5: 221-34. ",
"absurl": "",
"email": "ares@biology.ucsc.edu"
},
{
"name": "3D-Footprint",
"url": "http://floresta.eead.csic.es/3dpwm/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1341",
"desc": "Estimates of DNA-binding specificity for protein-DNA complexes in PDB",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D91",
"email": "footprint3d@yahoo.es"
},
{
"name": "ABS",
"url": "http://genome.crg.es/datasets/abs2005/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/795",
"desc": "ABS (Annotated Binding Sites) is a public database of experimentally verified orthologous transcription factor binding sites (TFBSs). Annotations have been collected from the literature and are manually curated. For each gene, the TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) have been always extracted to form the collection of gene promoter sequences from human, mouse, rat and chicken.For each one of the annotated 650 regulatory sites, the position, the motif and the sequence in which the site is present are available in a very simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments, and graphical dotplots are also available. ABS is oriented to the study of regulatory regions in the context of pattern discovery programs. Thus, ABS provides two applications to aid during the automatical training of them: CONSTRUCTOR and EVALUATOR.\nCONSTRUCTOR automatically generates artificial benchmarks by planting motifs in random sequences. The user can customize the content of the background sequence, the number of motifs that are planted, the subset of the real sites that can be used, the density of motifs on each sequence, and the length and the number of the sequences.EVALUATOR uses the standard accuracy measures to assess the correctness of the predictions introduced by the user in contrast to the real sites also submitted. In the output, a table with the accuracy at both nucleotide and site level is supplied. The formal definitions of the values are always included to facilitate the interpretation.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D63",
"email": "eblanco@imim.es"
},
{
"name": "ACTIVITY",
"url": "http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/231",
"desc": "ACTIVITY, a database on DNA site sequences with known activity magnitudes, measurement systems and sequence-activity relationships under fixed experimental conditions is additionally adapted to applications to the phylogenetic footprints of known sites. To this aim, we have created three resources, ACTIVITY_Reports, ACTIVITY_Tuning, and TFsite_Annotations. For a given site with known sequence-activity relationships, the first database ACTIVITY_Reports accumulates the quantitative data on the impact of the site surrounding, which allows for correct recognition of this site. From this way characterized site-surrounding relationships, the Java applet aimed at precise analysis of phylogenetic footprints of only this known site is automatically generated and stored within the knowledge base ACTIVITY_Tuning. Next, the resulting database TFsite_Annotations documents the Java applet results obtained in the cases of only putative sites of the same type and the same location within the same regulatory region of the homologous gene. The resources enriching the current ACTIVITY release are available at URL=http://util.bionet.nsc.ru/databases/activity.html.",
"ref": " Mulligan,M., Hawley,D., Entriken,R. and McClure,W. (1984) Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res., 12, 789-800.Ponomarenko,J., Furman,D., Frolov,A., Podkolodny,N., Orlova,G., Ponomarenko,M., Kolchanov,N. and Sarai,A. (2001) ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. Nucleic Acids Res., 29, 284-287.Wingender,E., Chen,X., Hehl,R., Karas,H., Liebich,I., Matys,V., Meinhardt,T., Pru?,M., Reuter,I. and Schacherer,F. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res., 28, 316-319.Kolchanov,N.A., Podkolodnaya,O.A., Ananko,E.A., Ignatieva,E.V., Stepanenko,I.L., Kel-Margoulis,O.V., Kel,A.E., Merkulova,T.I., Goryachkovskaya,T.N., Busygina,T.V. et al., (2000) Transcription regulatory regions database (TRRD): its status in 2000. Nucleic Acids Res. 28, 298-301.Jonsson,J., Norberg,T., Carlsson,L., Gustafsson,C. and Wold,S. (1993) Quantitative sequence-activity models (QSAM) - tools for sequence design. Nucleic Acids Res., 21, 733-739.Berg,O.G. and von Hippel,P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750Berg,O.G. and von Hippel,P.H. (1988) Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol., 200, 709-723. Barrick,D., Villanueba,K., Childs,J., Kalil,R., Schneider,T.D., Lawrence,C.E., Gold,L. and Stormo,G.D. (1994) Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res., 22, 1287-1295.Stormo,G.D., Schneider,T.D. and Gold,L. (1986) Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res., 14, 6661-6679.Ponomarenko,M., Kolchanova,A. and Kolchanov,N. (1997) Generating programs for predicting the activity of functional sites. J Comput Biol, 4, 83-90. Kraus,R.J., Murray,E.E., Wiley,S.R., Zink,N.M., Loritz,K., Gelembiuk,G.W. and Mertz,J.E. (1996) Experimentally determined weight matrix definitions of the initiator and TBP binding site elements of promoters. Nucleic Acids Res., 24, 1531-1539.Ponomarenko,M., Ponomarenko,J., Frolov,A., Podkolodny,N., Savinkova,L., Kolchanov,N. and Overton,G.C. (1999) Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinformatics, 15, 687-703.Takeda,Y., Sarai,A. and Rivera,V.M. (1989) Analysis of the sequence-specific interactions between Cro repressor and operator DNA by systematic base substitution experiments. Proc. Natl. Acad. Sci. U.S.A., , 439-443.Sarai,A. and Takeda,Y. (1989) Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc. Natl. Acad. Sci. U.S.A., 86, 6513-6517.Hao,D., Ohme-Takagi,M. and Sarai,A. (1998) Unique mode of GCC box recognition by the DNA-binding domain of ethylene-responsive element-binding factor (ERF domain) in plant. J. Biol. Chem., 273, 26857-26861.Tanikawa,J., Yasukawa,T., Enari,M., Ogata,K., Nishimura,Y., Ishii,S. and Sarai,A. (1993) Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain. Proc. Natl. Acad. Sci. U.S.A., 90, 9320-9324.Ogata,K., Kanei-Ishii,C., Sasaki,M., Hatanaka,H., Nagadoi,A., Enari,M., Nakamura,H., Nishimura,Y., Ishii,S. and Sarai,A. (1996) The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation. Nat. Struct. Biol., 3, 178-187.McCormick,A., Brady,H., Fukushima,J. and Karin,M., (1991) The pituitary-specific regulatory gene GHF1 contains a minimal cell type-specific promoter centered around its TATA box. Genes Dev., 5, 1490-1503.Javahery,R., Khachi,A., Lo,K., Zenzie-Gregory,B. and Smale,S.T. (1994) DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol. Cell. Biol., 14, 116-127.Hyde-DeRuyscher,R., Jennings,E. and Shenk,T. (1995) DNA binding sites for the transcriptional activator/repressor YY1. Nucleic Acids Res., 23, 4457-4465.Ludlow,L.B., Schick,B.P., Budarf,M.L., Driscoll,D.A., Zackai,E.H., Cohen,A. and Konkle,BA. (1996) Identification of a mutation in a GATA binding site of the platelet glycoprotein Ibbeta promoter resulting in the Bernard-Soulier syndrome. J. Biol. Chem., 271, 22076-22080.Roulet,E., Bucher,P., Schneider,R., Wingender,E., Dusserre,Y., Werner,T. and Mermod,N. (2000) Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J. Mol. Biol., 297, 833-848.Tsutsumi-Ishii,Y., Tadokoro,K., Hanaoka,F. and Tsuchida,N. (1995) Response of heat shock element within the human HSP70 promoter to mutated p53 genes. Cell Growth Differ., 6, 1-8.Ponomarenko,J., Merkulova,T., Vasiliev,G., Levashova,Z., Orlova,G., Lavryushev,S., Fokin,O., Ponomarenko,M., Frolov,A. and Sarai,A. (2001) rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Res., 29, 312-316.Ponomarenko,J., Merkulova,T., Orlova,G., Fokin,O., Gorshkova,E. and Ponomarenko,M. Mining DNA sequences to predict sites which mutations cause genetic diseases. (2002) Knowledge-Based Systems. 15, 225-233. Lardans,V., Ram,D., Lantner,F., Ziv,E. and Schechter,I. (2001) Differences in DNA-sequence recognition between the DNA-binding domain fragment and the full-length molecule of the heat-shock transcription factor of schistosome. Biochim Biophys Acta, 1519, 230-234.Tachibana,T., Astumi,S., Shioda,R., Ueno,M., Uritani,M., Ushimaru,T. (2002) A novel non-conventional heat shock element regulates expression of MDJ1 encoding a DnaJ homolog in Saccharomyces cerevisiae. J Biol Chem., 277, 22140-22146. ",
"absurl": "",
"email": "jpon@bionet.nsc.ru"
},
{
"name": "AGRIS - <i>Arabidopsis</i> Gene Regulatory Information Server",
"url": "http://arabidopsis.med.ohio-state.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/618",
"desc": "AGRIS is an information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS currently contains two databases, AtTFDB (Arabidopsis thaliana transcription factor database) and AtcisDB (Arabidopsis thaliana cis-regulatory database). AtTFDB contains information on approximately 1,500 transcription factors identified through motif searches and grouped into families, based on the presence of conserved domains. AtTFDB links the sequence of the transcription factors with available mutants and, when known, with the possible genes they may regulate. AtcisDB consists of the 5' regulatory sequences of all 29,388 annotated genes with a description of the corresponding cis-regulatory elements. Users can search the databases for (i) promoter sequences, (ii) a transcription factor, (iii) a direct target gene for a specific transcription factor, or (vi) a regulatory network that consists of transcription factors and their target genes.",
"ref": "",
"absurl": null,
"email": "yilmaz.11@osu.edu"
},
{
"name": "AnimalTFDB",
"url": "http://115.156.249.50/TFDB/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1460",
"desc": "Animal Transcription Factor Database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D144",
"email": "guoay@hust.edu.cn"
},
{
"name": "ASPD",
"url": "http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/308",
"desc": "ASPD is a new curated database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution process (mainly by means of phage display technique). ASPD database is being compiled by curating the scientific literature. At present, it contains data on 200 selection experiments, which were described in 150 original papers. For each experiment, the following information is given: description of the target for binding; description of the protein or peptide which serves as the template for library construction and description of the native protein which binds the target; links to the major proteomic databases – SwissProt, PDB, Prosite and Enzyme; keywords referring to the biological significance of the experiment; aligned sequences of proteins or peptides retrieved through in vitro evolution and relevant native or constructed sequences; the number of rounds of selection/amplification cycles and the number of occurences of clones with each sequence. The literature data include full reference, link to Medline database and the name of corresponding author with his e-mail. ASPD has a user-friendly interface which allows for simple queries using the names of proteins and ligands, as well as keywords describing the biological role of the interaction studied, and also for queries based on author names. The other possibility to access the database is that by means of the SRS system which allows complex queries. There is also a BLAST search tool against the ASPD for looking directly for homologous sequences. Direct data submission to the ASPD is welcome via the submission form available at the ASPD Web-page. Research tools of the ASPD comprise the analysis of pairwise correlations in the alignment of sequences of proteins and peptides selected against one target. We have calculated such correlations in terms of hydrophobicity , polarity, volume and isoelectric point. The amino acid similarity matrix based on the data stored in the ASPD was also derived and compared with other similar matrices.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/30/1/200",
"email": "valuev@bionet.nsc.ru"
},
{
"name": "BloodChIP",
"url": "http://149.171.101.136/python/BloodChIP/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1675",
"desc": "Transcription factor binding profiles in human haematopoietic stem/progenitor cells",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D172",
"email": "jpimanda@unsw.edu.au"
},
{
"name": "ChIPBase",
"url": "http://deepbase.sysu.edu.cn/chipbase/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1594",
"desc": "Decoding transcriptional regulation of lncRNA and microRNA genes from ChIP-Seq data",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1060",
"email": "lssqlh@qq.com"
},
{
"name": "cisRED",
"url": "http://www.cisred.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/805",
"desc": "cisRED (http://www.cisred.org) is a database for predicted regulatory elements that are identified and ranked by a computational system for genome-scale discovery of phylogenetically conserved motifs. The current version of the database, human v2, contains 386 000 motifs with lengths between 6 to ~30 base pairs. Motifs were predicted for ~18 000 human genes, using sequence search regions that extended from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons, which were masked. Many known transcription factor binding sites are located in such regions. Motifs were predicted using multiple de novo discovery methods applied to multi-species sequence sets that contained between 4 and 15 vertebrate species. An empirical p-value was assigned to each motif by applying motif discovery methods to randomized sequence sets that were adaptively derived from target sequence sets, and retaining motifs below a p-value threshold. Groups of similar motifs were identified using OPTICS hierarchical clustering; co-occurring patterns of motifs are being identified. Predicted regulatory elements can be viewed directly in cisRED's web user interface, and can be user-filtered by p-value or species composition. In addition, motifs can be viewed in the UCSC or Ensembl genome browsers, and in the Sockeye comparative genomics workspace. Methods are described by documentation on the cisRED web site. A schema diagram is available, and the data and SQL structure for the MySQL databases can be downloaded. The database can be queried directly at db.cisred.org, using \"anonymous\" as a username and leaving the password blank.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D68",
"email": "grobertson@bcgsc.ca"
},
{
"name": "CMGSDB",
"url": "https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1058",
"desc": "Computational models for gene silencing in C. elegans",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D69",
"email": "apati@vt.edu"
},
{
"name": "CollecTF",
"url": "http://collectf.umbc.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1676",
"desc": "Experimentally-verified bacterial transcription factor binding sites",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D156",
"email": "erill@umbc.edu"
},
{
"name": "CoryneRegNet",
"url": "http://coryneregnet.cebitec.uni-bielefeld.de/v6/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1167",
"desc": "CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks.",
"ref": "1. Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A. (2007) CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. J Biotechnol. 2007 (in press, http://dx.doi.org/10.1016/j.jbiotec.2006.12.012).2. Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S (2006) CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. Journal of Integrative Bioinformatics, 3(2):24, 2006.3. Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A (2006) CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics. 2006 Feb 14;7(1):24. (http://www.biomedcentral.com/1471-2164/7/24).",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D610",
"email": "Jan.Baumbach@CeBiTec.Uni-Bielefeld.DE"
},
{
"name": "COXPRESdb",
"url": "http://coxpresdb.jp/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1062",
"desc": "Coexpressed genes and networks in human and mouse",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D77",
"email": "obayashi@hgc.jp"
},
{
"name": "CTCF Binding Site Database",
"url": "http://insulatordb.uthsc.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1063",
"desc": "Experimentally identified and predicted CTCF binding sties",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D83",
"email": "ycui2@utmem.edu"
},
{
"name": "DBD",
"url": "http://www.transcriptionfactor.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/807",
"desc": "DBD provides transcription factor predictions for more than 150 completely sequenced genomes available for browsing and download. Predictions are based on presence of sequence specific DNA binding domain assignments using hidden Markov models from the SUPERFAMILY and PFAM databases. Evaluation shows that our predictions are 97% accurate and give at least 65% coverage. Focusing on individual genomes show that DBD identifies many novel factors for example, corresponding to a 90% increase in the known mouse transcription factor repertoire. Users can browse factors by genome or domain type, search for particular factors or submit a sequence for prediction.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D88",
"email": "skk@mrc-lmb.cam.ac.uk"
},
{
"name": "DBTBS",
"url": "http://dbtbs.hgc.jp/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/31",
"desc": "With the entire genome sequence of Bacillus subtilis now determined, one of the next major targets of B. subtilis genomics is to elucidate its complete gene regulatory network. To this end, the results of systematic experiments should be compared with the rich source of individual experimental results accumulated so far. We therefore constructed the DBTBS database, containing a collection of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of B. subtilis genes. Its current version is constructed by surveying 873 references and contains the information of 116 binding factors and 1253 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. Multiple alignments of upstream sequences between B. halodurans, B. stearothermophilus, and B. subtilis are also shown.",
"ref": "1. Ishii, T. et al. (2001). Nucleic Acids Res. 29, 278-280.2. Makita, Y. et al. (2004). Nucleic Acids Res. 32, D75-D77",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D75",
"email": "knakai@ims.u-tokyo.ac.jp"
},
{
"name": "DBTSS",
"url": "http://dbtss.hgc.jp/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/591",
"desc": "DBTSS is a collection of transcriptional start sites and adjacent promoters, which are experimentally determined by intensive analyses of full-length cDNAs. In order to extract biological insight from the compiled sequence information, search engines for putative transcription factor binding sites are implemented. Also, for molecular evolutionary studies of the transcriptional regulations, detailed sequence alignments of the promoters between human, mouse and other model organisms are provided. DBTSS is available on the web in Japan at http://dbtss.hgc.jp, in Germany at http://dbtss.bioinf.med.uni-goettingen.de/ and in Poland at http://tarawa.icm.edu.pl/dbtss/. The positional information of the TSSs, sequences of the promoters and related information can also be downloaded in flatfile form from the download site. The current release of DBTSS (5.1) contains TSS information of 15262 and 14162 genes determined by 1.4 and 0.4 million cDNAs in humans and mice, respectively.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D150",
"email": "ysuzuki@ims.u-tokyo.ac.jp"
},
{
"name": "DoOP - Databases of Orthologous Promoters",
"url": "http://doop.abc.hu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/663",
"desc": "DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically.This work was supported by Biotechnology 2001 grant BIO-0117/01 from the Central Technical Development Target Funds (Hungary). B.E. and G.T. were recipients of 'Bolyai Fellowship’ awarded by the Hungarian Academy of Sciences.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D86",
"email": "barta@abc.hu"
},
{
"name": "DPInteract",
"url": "http://arep.med.harvard.edu/dpinteract/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/106",
"desc": "Binding sites for E. coli DNA-binding proteins",
"ref": "1. Robison K, McGuire AM, Church GM. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol. 1998, 284: 241-254.",
"absurl": "",
"email": "krobison@nucleus.harvard.edu"
},
{
"name": "DPRP",
"url": "http://syslab.nchu.edu.tw/DPRP/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1677",
"desc": "A database of phenotype-specific regulatory programs derived from transcription factor binding data",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D178",
"email": "chao.cheng@dartmouth.edu"
},
{
"name": "ECRbase",
"url": "http://ecrbase.dcode.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1157",
"desc": "Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and Fugu genomes. It is freely accessible at http://ecrbase.dcode.org",
"ref": "G.G. Loots and I. Ovcharenko, ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes, Bioinformatics, 23(1):122-4 (2007)",
"absurl": "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/1/122",
"email": "ovcharei@ncbi.nlm.nih.gov"
},
{
"name": "EPD",
"url": "http://epd.vital-it.ch/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/33",
"desc": "The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. WWW-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extrac promoter sequences according to a variety of criteria, and to navigate to related databases exploiting different cross-references. The EPD web site also features yearly updated base frequency matrices for major eukaryotic promoter elements.",
"ref": "Praz, V., PÉrier, R., Bonnard, C., Bucher, P. (2002). The Eukaryotic Promoter Database EPD: New entry types and links gene expression data. Nucleic Acids Res. 30, 322-324",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D82",
"email": "epd@mail.isrec.isb-sib.ch"
},
{
"name": "Factorbook",
"url": "http://www.factorbook.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1595",
"desc": "Human transcription factor binding data from ChIP-seq",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1221",
"email": "Zhiping.Weng@umassmed.edu"
},
{
"name": "FlyFactorSurvey",
"url": "http://pgfe.umassmed.edu/TFDBS/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1312",
"desc": "Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D111",
"email": "Michael.Brodsky@umassmed.edu"
},
{
"name": "FlyTF",
"url": "http://www.flytf.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1158",
"desc": "FlyTF (v2) is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified TFs from the literature.",
"ref": "1. Adryan, B. and Teichmann, S.A. (2006) FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics 22(12), 1532\n2. Adryan, B. and Teichmann, S.A. (2007) Computational Identification of Site-Specific Transcription Factors in Drosophila. Fly 1(3), 142",
"absurl": "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/12/1532",
"email": "ba255@cam.ac.uk"
},
{
"name": "GeneNet",
"url": "http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/329",
"desc": "The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways, and kinetic characteristics of elementary processes. In the past two years, the GeneNet structure was considerably improved: 1) the current version of the database is now implemented using ORACLE9i; 2) the capacities to describe the structure of the protein complexes and the interactions between the units are increased; 3) two tables with kinetic constants and more detailed descriptions of certain reactions were added; 4) a module for kinetic modeling was supplemented.The current SRS release of the GeneNet database contains 37 graphical maps of gene networks, as well as descriptions of 1766 proteins, 1006 genes, 241 small molecules, and 3254 relationships between gene network units, and 552 kinetic constants. Information distributed between 16 interlinked tables was obtained by annotating 1980 journal publications. SRS release of the GeneNet database, the graphical viewer, and the modeling section are available at http://wwwmgs.bionet.nsc.ru/mgs/systems/genenet/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D425",
"email": "eananko@bionet.nsc.ru"
},
{
"name": "GenomeTraFaC",
"url": "http://genometrafac.cchmc.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1036",
"desc": "Adopting a systematic gene-centric pipeline approach, GenomeTraFaC (http://genometrafac.cchmc.org) allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes.Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures.The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures.Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D116",
"email": "bruce.aronow@cchmc.org"
},
{
"name": "Greglist",
"url": "http://tubic.tju.edu.cn/greglist/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1082",
"desc": "G-quadruplex motifs and potentially G-quadruplex regulated genes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D372",
"email": "ctzhang@tju.edu.cn"
},
{
"name": "HOCOMOCO",
"url": "http://autosome.ru/HOCOMOCO",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1596",
"desc": "HOmo sapiens COmprehensive MOdel COllection of hand-curated transcription factor binding site models",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1089",
"email": "ivan.kulakovskiy@gmail.com"
},
{
"name": "HTPSELEX",
"url": "http://ccg.vital-it.ch/htpselex/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/823",
"desc": "Transcription factor binding site sequences obtained using high-throughput SELEX method",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D90",
"email": "Philipp.Bucher@isrec.unil.ch"
},
{
"name": "JASPAR",
"url": "http://jaspar.genereg.net/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/516",
"absurl": null,
"email": null
},
{
"name": "MachiBase",
"url": "http://machibase.gi.k.u-tokyo.ac.jp/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1224",
"desc": "Drosophila melanogaster 5' mRNA transcription start site database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D49",
"email": null
},
{
"name": "MAPPER",
"url": "http://genome.ufl.edu/mapperdb/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/700",
"desc": "Putative transcription factor binding sites in various genomes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D155",
"email": null
},
{
"name": "MPromDB",
"url": "http://bioinformatics.wistar.upenn.edu/MPromDb/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/842",
"desc": "Mammalian promoter database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D98",
"email": "rdavuluri@wistar.org"
},
{
"name": "ODB - Operon database",
"url": "http://operondb.jp/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/846",
"desc": "ODB (Operon DataBase) is a database of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The first release of ODB conteins about 2000 known operons and 13,000 putative operons in more than 200 genomes. ODB is accessible from http://odb.kuicr.kyoto-u.ac.jp/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D358",
"email": "okd@sk.ritsumei.ac.jp"
},
{
"name": "OnTheFly",
"url": "http://bhapp.c2b2.columbia.edu/OnTheFly/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1678",
"desc": "DNA-binding specificities of transcription factors in Drosophila",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D167",
"email": "ss4179@columbia.edu"
},
{
"name": "ooTFD",
"url": "http://www.ifti.org/ootfd",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/185",
"desc": "ooTFD (1) is a database of transcription factors maintained in object-oriented and object-relational database systems. There are, at the time of this writing, about 7500 TF binding sites entries in this database, from both prokaryotic and eukaryotic sources, as well as roughly 500 TF binding site matrices. A number of tools and services are available for commonly performed sequence analyses against these datasets, as well as for the performing of ooTfd database queries are provided at the IFTI-MIRAGE web site. Matrix entries in this database are given a quality score according to the statistical methodology described by Rahmann et.al. (2), which may be utilized in the interpretation of matrix-based TF binding site searches. Entries in this database resource are linked, either through hard links based on published experimental results, or through precomputed datasets, to entries in EPD (3), PKR (4), and PDB (5). ooTFD and associated utilities can be accessed at http://www.ifti.org/ootfd/ .",
"ref": "1. Ghosh D (2000) Object-oriented transcription factors database (ooTFD). Nucleic Acids Res 28: 308-10.2. Rahmann S, T Muller, M Vingron (2003) On the Power of Profiles for Transcription Factor Binding Site Detection. Statistical Applications in Genetics and Molecular Biology 2.1: art7.3. Praz V, R Perier, C Bonnard, P Bucher (2002) The Eukaryotic Promoter Databbase, EPD: new entry types and links to gene expression data. Nucleic Acids Res 30: 322-4.\n4. Smith CM, IN Shindyalov, S Veretnik, M Gribskov, SS Taylor, LF TenEyck, P Bourne (1997) The Protein Kinase Resource. Trends Biochem Sci 22: 444-6.5. Berman HM, J Westbrook, Z Fend, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, P Bourne (2000) Nucleic Acids Res 28: 235-42.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/28/1/308",
"email": "dghosh@ifti.org"
},
{
"name": "ORegAnno",
"url": "http://www.oreganno.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1107",
"desc": "Open REGulatory ANNOtation database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D107",
"email": "obig@bcgsc.ca"
},
{
"name": "PAZAR",
"url": "http://www.pazar.info/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1258",
"desc": "Transcription factors and regulatory sequence annotations",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D54",
"email": null
},
{
"name": "PLACE",
"url": "http://www.dna.affrc.go.jp/PLACE/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/40",
"desc": "PLACE database now contains 380 entries of cis-element motifs found in plant genes. Increase in volume size for the new service at Plant cis-element (PLACE) database. There used to be a limit of 1,000 KB (=1MB) in total number of nucleotides in the queries for the upload version of SignalScan program. This is because our PLACE/SignalScan system shares the disk with other systems. On April 21, the limit was changed to 1,000 MB (=1 GB). Now user can submit batches of sequences up to 1,000MB in total volume size. This roughly means now user can submit all the Arabidopsis 25,000 putative promoter sequences the length of which is about 1,000 bp each. Each query sequence must be in FASTA format, and less than 4,356 bp.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/27/1/297",
"email": "kenhigo@nias.affrc.go.jp"
},
{
"name": "Plant Stress-Responsive Gene Catalog",
"url": "http://dayhoff.generationcp.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1116",
"desc": "Stress-responsive gene in various plant species",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D943",
"email": "R.BRUSKIEWICH@CGIAR.ORG"
},
{
"name": "PlantCARE",
"url": "http://bioinformatics.psb.ugent.be/webtools/plantcare/html/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/41",
"desc": "PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC (Wingender, E. et al.) and MEDLINE databases are provided where available. Data about the transcription sites are mainly extracted from the literature, added with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor (TF) sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are also given. New features have been implemented to search for plant cis-acting regulatory elements in a query sequence. Furthermore, links are now provided to a new clustering (De Smet, F. et al.) and motif search method to investigate clusters of co-expressed genes (Thijs, G. et al.). New regulatory elements can be sent automatically and added to the database after curation. At present, we have collected in total 668 cis-acting regulatory elements that can be queried on TF-site name, motif, function, species, cell type, gene, transcription factor, and literature references. These queries result in a listing of entries with links to other information within the database or beyond through accession numbers from other databases. The PlantCARE relational database is available via the WWW at the URL: http://intra.psb.ugent.be:8080/PlantCARE/index.html",
"ref": "1. Wingender,E., Chen,X., Hehl,R., Karas,H., Liebich,I., Matys,V., Meinhardt,T., PrÜß,M., Reuter,I. and Schacherer.F. (2000) TRANSFAC: an integrated system for gene expression regulation Nucleic Acids Res., 28, 316-319.2. Thijs,G., Marchal,K., Lescot,M., Rombauts,S., De Moor,B., Rouze,P., Moreau,Y. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol., 9:447-64. Thijs,G., Lescot,M., Marchal,K., Rombauts,S., De Moor,B.,Moreau,Y. and Rouze, P. (2001) A higher order background model improves the detection by Gibbs sampling of potential promoter regulatory elements in DNA sequences. Bioinformatics., 17:1113-22.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/30/1/325",
"email": "stephane.rombauts@psb.ugent.be"
},
{
"name": "PlantProm",
"url": null,
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/563",
"absurl": null,
"email": null
},
{
"name": "PReMod",
"url": "http://genomequebec.mcgill.ca/PReMod/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1005",
"desc": "The PReMod database describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide/transcription factor-wide collection of predicted regulatory modules for the human genome.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D122",
"email": "blanchem@mcb.mcgill.ca"
},
{
"name": "PRODORIC",
"url": "http://prodoric.tu-bs.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/566",
"desc": "Prokaryotic database of gene regulation and regulatory networks",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D61",
"email": null
},
{
"name": "PromEC",
"url": "http://margalit.huji.ac.il/promec/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/42",
"desc": "E. coli mRNA promoters with experimentally identified transcriptional start sites",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/29/1/277",
"email": "hanah@md2.huji.ac.il"
},
{
"name": "ProTISA",
"url": "http://mech.ctb.pku.edu.cn/protisa/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1123",
"desc": "Translation Initiation Site Annotation in prokaryotic genomes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D114",
"email": "hugangqing@ctb.pku.edu.cn"
},
{
"name": "PTM-Switchboard",
"url": "http://cagr.pcbi.upenn.edu/PTMswitchboard/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1243",
"desc": "Post-translational modifications of yeast transcription factors",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D66",
"email": null
},
{
"name": "QuadBase",
"url": "http://quadbase.igib.res.in/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1126",
"desc": "G-quadruplex motifs in the promoters of human, chimpanzee, rat, mouse and bacterial genes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D381",
"email": "shantanuc@igib.res.in"
},
{
"name": "REDfly",
"url": "http://redfly.ccr.buffalo.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1128",
"desc": "Regulatory modules and transcription factor binding sites in Drosophila",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D594",
"email": "mshalfon@buffalo.edu"
},
{
"name": "RegPrecise",
"url": "http://regprecise.lbl.gov/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1342",
"desc": "Predicted regulons in prokaryotic genomes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D111",
"email": "psnovichkov@lbl.gov"
},
{
"name": "RegulonDB",
"url": "http://regulondb.ccg.unam.mx/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/116",
"desc": "RegulonDB is a database on mechanisms of transcription regulation, operon organization and knowledge on physiological conditions under which genes are induced or repressed in Escherichia coli K-12. The current version has an important increase in all objects of the database, regulons, operons, promoters, binding sites, regulatory proteins, their allosteric conformations, and terminators. It also has novel information about affected genes and the associated conditions of growth of E. coli, even if in many cases very little is known about the regulatory mechanism. Furthermore, a major improvement is a graphical display enabling browsing of the database with a Java-based interactive interface with three zoom-levels connected to properties of each chromosomal element. RegulonDB can be accessed on the web at http://www.cifn.unam.mx/Computational_Genomics/regulondb/.",
"ref": "",
"absurl": null,
"email": "ecoli-t1@cifn.unam.mx"
},
{
"name": "rSNP Guide",
"url": "http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/45",
"desc": "We have earlier developed the computer system and the database, rSNP_Guide, devoted to prediction of transcription factor (TF) binding sites, alterations of which are responsible for disease phenotype [Nucleic Acids Res. 29(1):312-316]. Then, with this system, the prediction results were obtained and, also, confirmed by 70 known relationships between TF sites and diseases, as well as by site-directed mutagenesis data. So that, for this current release presented, the rSNP_Guide is next considered as a tool for TF site annotation. Previously analyzed and characterized cases of altered TF sites are used to annotate potential sites of the same type and at the same location in homologous genes. Based on 20 TF sites with known alterations in TF binding to DNA, we have localized 245 potential TF sites in homologous genes. For these potential TF sites, rSNP_Guide estimates TF-DNA interaction according to three categories: 'present', 'weak', and 'absent'. The significance of each assignment is statistically measured. The present rSNP_Guide issue is at URL=http://util.bionet.nsc.ru/databases/rsnp.html.",
"ref": "Benson,D., Karsch-Mizrachi,I., Lipman,D., Ostell,J., Rapp,B. and Wheeler,D. (2002) GenBank. Nucleic Acids Res. 30, 17-20.3. Zdobnov,E., Lopez,R., Apweiler,R. and Etzold,T. (2002) The EBI SRS server-new features. Bioinformatics. 18, 1149-1150.4. Krawczak,M., Ball,E., Fenton,I., Stenson,P., Abeysinghe,S., Thomas,N. and Cooper,D. (2000) Human gene mutation database-a biomedical information and research resource. Hum. Mutat., 15, 45-51.5. Smigielski,E., Sirotkin,K., Ward,M. and Sherry,S.T. (2000), dbSNP: a database of single nucleotide polymorphisms, Nucleic Acids Res., 28, 352-355.6. Brookes,A., Lehvaslaiho,H., Siegfried,M., Boehm,J., Yuan,Y., Sarkar,C., Bork,P. and Ortiga F. (2000) HGBASE: a database of SNPs and other variations in and around human genes, Nucleic Acids Res., 28, 356-360.7. Cheung,K., Osier,M., Kidd,J., Pakstis,A., Miller,P. and Kidd,K. (2000) ALFRED: an allele frequency database for diverse populations and DNA polymorphisms. Nucleic Acids Res., 28, 361-363.8. McKusick,V. (1998) Mendelian Inheritance in Man. Catalogs of human genes and genetic disorders, Johns Hopkins University Press, Baltimore9. Vasiliev,G., Merkulov,V., Kobzev,V., Merkulova,T., Ponomarenko,M. and Kolchanov,N. (1999) Point mutations within 663-666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site. FEBS Lett., 462, 85-88.10. Knight,J., Udalova,I., Hill,A., Greenwood,B., Peshu,N., Marsh,K. and Kwiatkowski,D. (1999) A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria. Nat Genet. 22, 145-150.11. Tsutsumi-Ishii,Y., Tadokoro,K., Hanaoka,F. and Tsuchida,N. (1995) Response of heat shock element within the human HSP70 promoter to mutated p53 genes. Cell Growth Differ. 6, 1-8.12. Langdon,S. and Kaufman,R. (1998) Gamma-globin gene promoter elements required for interaction with globin enhancers. Blood, 91, 309-318.13. Quandt,K., Frech,K., Karas,H., Wingender,E. and Werner,T. (1995) MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 23, 4878-4884.14. Roulet,E., Bucher,P., Schneider,R., Wingender,E., Dusserre,Y., Werner,T. and Mermod,N. (2000) Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J Mol Biol. 297, 833-848. Mandel-Gutfreund,Y., Baron,A. And Margalit,H. (2001) A structure-based approach for prediction of protein binding sites in gene upstream regions. Pac Symp Biocomput., 139-150. Wasserman,W. and Fickett,J. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol. 278, 167-181. Wasserman,W., Palumbo,M., Thompson,W., Fickett,J. and Lawrence,C. (2000) Human-mouse genome comparisons to locate regulatory sites. Nat Genet. 26, 225-228. Ponomarenko,J., Merkulova,T., Vasiliev,G., Levashova,Z., Orlova,G., Lavryushev,S., Fokin,O., Ponomarenko,M., Frolov,A. and Sarai,A. (2001) rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Res. 29, 312-316. Ponomarenko,J., Merkulova,T., Orlova,G., Fokin,O., Gorshkova,E. and Ponomarenko,M. Mining DNA sequences to predict sites which mutations cause genetic diseases. (2002) Knowledge-Based Systems. 15, 225-233. Jeunemaitre,X., Soubrier,F., Kotelevtsev,Y., Lifton,R., Williams,C., Charru,A., Hunt,S., Hopkins,P., Williams,R., Lalouel,J. et al. (1992) Molecular basis of human hypertension: role of angiotensinogen. Cell, 71, 169-180. Zhao,Y., Zhou,J., Narayanan,C., Cui,Y. and Kumar,A. (1999) Role of C/A polymorphism at -20 on the expression of human angiotensinogen gene. Hypertension, 33, 108-115. Klinge,C. (2001) Estrogen receptor interaction with estrogen response elements. Nucleic Acids Res. 29, 2905-2919. Narayanan,C., Cui,Y., Zhao,Y., Zhou,J. and Kumar,A. (1999) Orphan receptor Arp-1 binds to the nucleotide sequence located between TATA box and transcriptional initiation site of the human angiotensinogen gene and reduces estrogen induced promoter activity. Mol Cell Endocrinol.148, 79-86.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/31/1/118",
"email": "jpon@bionet.nsc.ru"
},
{
"name": "ScerTF",
"url": "http://stormo.wustl.edu/ScerTF",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1461",
"desc": "Binding sites for Saccharomyces cerevisiae Transcription Factors",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D162",
"email": "aaspivak@ural.wustl.edu"
},
{
"name": "SCPD - Saccharomyces cerevisiae promoter database",
"url": "http://rulai.cshl.edu/SCPD/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/577",
"desc": "A database of yeast promoters",
"ref": "1. Zhu J, Zhang MQ. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics. 1999 Jul-Aug;15(7-8):607-11.",
"absurl": "",
"email": null
},
{
"name": "SELEXdb",
"url": "http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/246",
"desc": "SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for these oligomers recognition. In vitro selection of oligomers binding target proteins is a novel technology intensively being developed during the last decade, for sieving a pool of synthetic oligomers through repeated cycles of PCR-amplification and protein-binding selection (1). According to Human Genome Annotation, we have developed the SELEX_DB database on oligomers selected in vitro, the database being supplied by Web-available applets for site recognition (2). Besides, since many disease may be caused not only by the mutation-altered transcription factor binding true-site on DNA, but also by the appearance of a novel protein-fitting noise-site altering a normal regulation of a gene network (e.g., the substitution -376G>A in human TNF gene promoter produces the transcription factor OCT-fitting noise-site causing the clinical phenotype 'severe malaria' (3)), the in vitro selected aptamers are very informative for the Single Nucleotide Polymorphism (SNP) analysis. At the same time, in prokaryota, the discrepancies between in vitro selected and natural sites by nucleotide-position frequency matrices have been comprehensively demonstrated (4). Besides, the positional Information Content matrices of the in vitro selected aptamers was found to be correlating with the protein-binding strength magnitudes, whereas neither correlation was found for the corresponding natural site (5). This means that, in prokaryota, natural sites were selected in vivo according to their biological activity, but not by protein affinity. In eukaryota, the relationship between in vivo and in vitro selections seems to be very knotty. From one hand, the in vitro selected TBP-binding DNAs provide the natural TATA-box activity (6). Moreover, homologous c-Myb and v-Myb proteins, minimal Myb/DNA-binding domain and, Myb-fortified cell nuclear extract are selecting in vitro the aptamers, similarities of which to one the others and to the natural c-Myb sites are significant (7). From the other hand, in vitro selected YY1-binding DNAs, inserted into the plasmids and transfected into various cells ('plasmid+cell' system), repress the reported gene (8), thus supporting the fact that YY1 binding strength and repression magnitudes do not correlate. Moreover, for these in vitro selected YY1-fitting aptamers, these YY1-caused repression measured in vivo at one 'plasmid+cell' system do not correlate to the proper magnitudes detected in vivo at the other 'plasmid+cell' system. According to this evident system-dependence of both in vitro and in vivo selected experimental data, nowadays a fundamental question is how in vitro selected data could be implemented for natural gene analysis (1). That is why novel release of the SELEX_DB has been supported by two databases SYSTEM (9, 10) and CROSS_TEST, storing both experiment systems and their cross-validation tests. By cross-validation testing, we have unexpectedly observed that, for a fixed protein-binding site, the recognition accuracy increases with the growth of homology between the target and test proteins. For natural sites, the recognition accuracy was less than for the nearest protein homologs and higher than for the distant homologs and non-homologous proteins binding the common site. The current SELEX_DB release is available at URL=http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/.",
"ref": null,
"absurl": null,
"email": "jpon@bionet.nsc.ru"
},
{
"name": "SKY/M-FISH and CGH",
"url": "http://www.ncbi.nlm.nih.gov/sky/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/592",
"desc": "The NCI and NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic Hybridization (CGH), which are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mouse chromosome in a different color, facilitating the identification of chromosomal aberrations; CGH can be used to generate a map of DNA copy number changes in tumor genomes. Collaborative project with the National Cancer Institute.",
"ref": null,
"absurl": "",
"email": "skycghweb@ncbi.nlm.nih.gov"
},
{
"name": "STIFDB2",
"url": "http://caps.ncbs.res.in/stifdb2",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1582",
"absurl": null,
"email": null
},
{
"name": "SwissRegulon",
"url": "http://www.swissregulon.unibas.ch/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1015",
"desc": "SwissRegulon (http://www.swissregulon.unibas.ch) is a database containing genome-wide annotations of regulatory sites in the intergenic regions of genomes. The regulatory site annotations are produced using a number of recently developed algorithms that operate on multiple alignments of orthologous intergenic regions from related genomes in combination with, whenever available, known sites from the literature, and ChIP-on-chip binding data. Currently SwissRegulon contains annotations for yeast and 17 prokaryotic genomes. The database provides information about the sequence, location, orientation, posterior probability and, whenever available, binding factor for each annotated site. To enable easy viewing of the regulatory site annotations in the context of other features annotated on the genomes, the sites are displayed using the GBrowse genome browser interface and can be queried based on any annotated genomic feature. The database can also be queried for regulons, i.e. sites bound by a common factor.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D127",
"email": "Erik.Vannimwegen@unibas.ch"
},
{
"name": "TcoF-DB",
"url": "http://cbrc.kaust.edu.sa/tcof/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1334",
"desc": "Database for Human Transcription Co-Factors",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D106",
"email": "vladimir.bajic@kaust.edu.sa"
},
{
"name": "Telomerase database",
"url": "http://telomerase.asu.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1137",
"desc": "Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D339",
"email": "JLChen@asu.edu"
},
{
"name": "TESS",
"url": "http://www.cbil.upenn.edu/cgi-bin/tess/tess",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/227",
"desc": "TESS (Transcription Element Search System, http://www.cbil.upenn.edu/tess) is a web-based service that searches DNA sequence for transcription factor binding sites. It integrates three databases of transcription factors and binding site models, and provides browsing and querying capability for the databases, sequence searching, and accuracy data for the positional weight matrix (PWM) models.",
"ref": null,
"absurl": "",
"email": "jschug@pcbi.upenn.edu"
},
{
"name": "TFBSshape",
"url": "http://rohslab.cmb.usc.edu/TFBSshape/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1679",
"absurl": null,
"email": null
},
{
"name": "TFClass",
"url": "http://tfclass.bioinf.med.uni-goettingen.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1571",
"desc": "TFClass (http://tfclass.bioinf.med.uni-goettingen.de/) provides a comprehensive classification of human transcription factors (TFs), based on their DNA-binding domains. Transcription factors constitute a large functional family of proteins directly regulating the activity of genes. Most of them are sequence-specific DNA-binding proteins, thus reading out the information encoded in cis-regulatory DNA elements of promoters, enhancers and other regulatory regions of a genome. TFClass updates earlier attempts to classify eukaryotic transcription factors (1, 2); it is a database that classifies (so far) human transcription factors by a six-level classification schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene products. With this classification, we hope to provide a basis for deciphering protein-DNA recognition codes; moreover, it can be used for constructing expanded transcriptional networks by inferring additional TF-target gene relations.",
"ref": "1.\tWingender,E. (1997) Classification of eukaryotic transcription factors. Mol. Biol. Engl. Tr., 31, 483-497.",
"absurl": null,
"email": "edgar.wingender@bioinf.med.uni.goettingen.de"
},
{
"name": "TiProD",
"url": "http://tiprod.bioinf.med.uni-goettingen.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/904",
"desc": "TiProD is a database of human promoter sequences for which some functional features are known. It allows a user to query individual promoters and the expression pattern they mediate, gene expression signatures of individual tissues, and to retrieve sets of promoters according to their tissue-specific activity or according to individual GO-terms the corresponding genes are assigned to. We have defined a measure for tissue-specificity that allows the user to discriminate between ubiquitously and specifically expressed genes",
"ref": null,
"absurl": null,
"email": "edgar.wingender@bioinf.med.uni-goettingen.de"
},
{
"name": "TRACTOR db",
"url": "http://www.tractor.lncc.br/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/756",
"desc": "Experimental data on the Escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, Transcription Factors (TFs), TFs' binding sites, operons) within its genome. As more genomes of gamma-proteobacteria are being sequenced, the prediction of these elements in a growing number of organisms has become more feasible, as a step towards the study of how different bacteria respond to environmental changes at the level of transcriptional regulation. In this work we present TRACTOR_DB (TRAnscription FaCTORsÿ predicted sites in prokaryotic genomes), a relational database that contains computational predictions of new members of 74 regulons in eight gamma-proteobacterial genomes. To produce these predictions we used a comparative genomics approach of which several proof-of-principle articles for large regulons have been published. Furthermore, we used the predictions stored in our database to assess the conservation of regulons' size across all the eight genomes and showed that a correlation exists between the conservation of a regulatory site and the structure of the Transcription Unit (TU) it regulates. TRACTOR_DB may be currently accessed at http://www.bioinfo.cu/database, http://www.tractor.lncc.br or at http://www.cifn.unam.mx/Computational_Genomics/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D132",
"email": null
},
{
"name": "TRANSCompel<sup>®</sup>",
"url": "http://www.gene-regulation.com/pub/databases.html#transcompel",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/345",
"absurl": null,
"email": null
},
{
"name": "TRANSFAC<sup>®</sup>",
"url": "http://www.gene-regulation.com/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/340",
"desc": "The TRANSFAC® databasehas been constructed to model the interaction of eukaryotic transcription factors with their DNA-binding sites and how this affects gene expression. At its core are the three tables FACTOR, SITE, and GENE. A link between FACTOR and SITE indicates the interaction (binding) between them. Experimental evidence for this interaction is given in the SITE entry in form of the method (gel shift, footprinting analysis, ...) which was used to show the binding and the cell from which the factor was derived (factor source). On the basis of those, method and cell, a quality value is given to describe the \"confidence\" with which a binding activity could be assigned to a specific factor. When a number of binding sites have been collected for a factor, the site sequences are aligned and nucleotide distribution matrices are derived (MATRIX). These matrices are used by the tool MatchTMto find potential binding sites in uncharacterized sequences, while PatchTM, another tool, uses the single sites (and IUPAC consensus sequences), which are stored in the SITE table. A new, third tool, P-MatchTMcombines now the strengths of the matrix-based and the pattern-based approaches. While the binding sites are grouped into matrices to find a common denominator for the binding specificity of a certain factor, the transcription factors themselves are classified according to their DNA-binding domains in the CLASS table, as well as in a hierarchical factor classification tree. In addition to the binding properties of the transcription factors lots of information on their structure, function and tissue specificity is collected. In the GENE entries the respective sites and their binding factors, as well as the composite elements from TRANSCompel®, are summarized. As some of the regulated genes encode transcription factors themselves, there are not only links from factors via sites to target genes, but also from genes to encoded factors and vice versa. Based on these links \"gene regulatory networks\" can be retrieved/constructed. The GENE table does not only connect information of TRANSFAC® and TRANSCompel®, but also of other of our databases like HumanPSDTM, S/MARtDBTM, or TRANSPATH®, a database on signaling networks, into which the factor-site-gene interactions of TRANSFAC® are fully integrated. And finally, the GENE entries serve as major linking source to a growing number of (other) external databases. Public versions of TRANSFAC® and the above mentioned programs are freely accessible for research groups from non-profit organizations at http://www.gene-regulation.com. The professional version of TRANSFAC®, which contains not only a larger data amount but also an extended functionality, including integrated versions of Match® and Patch® as well as a tool for visualization of gene regulatory networks, is available at http://www.biobase-international.com.",
"ref": "1. Wingender,E. (1988) Compilation of transcription regulating proteins. Nucleic Acids Res., 16, 1879-1902.\n2. Wingender,E., Heinemeyer,T. and Lincoln,D. (1991) In Collins,J. and Driesel,A.J. (eds), Genome Analysis - From Sequence to Function; BioTechForu - Advances in Molecular Genetics. HÜthig Buch Verlag, Heidelberg, Vol. 4, pp. 95-108.\n3. KnÜppel,R., Dietze,P., Lehnberg,W., Frech, K. and Wingender,E. (1994) TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins. J. Comput. Biol., 1, 191-198.\n4. Wingender,E., Dietze,P., Karas,H. and KnÜppel,R. (1996) TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Res., 24, 238-241.\n5. Wingender,E., Kel,A.E., Kel,O.V., Karas,H., Heinemeyer,T., Dietze,P., KnÜppel,R., Romaschenko,A.G. and Kolchanov,N.A. (1997) TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res., 25, 265-268.\n6. Heinemeyer,T., Wingender,E., Reuter,I., Hermjakob,H., Kel,A.E., Kel,O.V., Ignatieva,E.V., Ananko,E.A., Podkolodnaya,O.A., Kolpakov,F.A., Podkolodny,N.L. and Kolchanov,N.A. (1998) Databases on transcriptional regulation: TRANSFAC, TRRD, and COMPEL. Nucleic Acids Res., 26, 362-367.\n7. Heinemeyer,T., Chen,X., Karas,H., Kel,A.E., Kel,O.V., Liebich,I., Meinhardt,T., Reuter,I., Schacherer,F. and Wingender,E. (1999) Expanding of the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res., 27, 318-322.\n8. Wingender,E., Chen,X., Hehl,R., Karas,H., Liebich,I., Matys,V., Meinhardt,T., PrÜß,M., Reuter,I. and Schacherer,F. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res., 28, 316-319.\n9. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., OhnhÄuser, R., PrÜß, M., Schacherer, F., Thiele, S. and Urbach, S. (2001). The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281-283\n10. Matys,V., Fricke,E., Geffers,R., GÖßling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V., Kloos,D.U., Land,S., Lewicki-Potapov,B., Michael,H., MÜnch,R., Reuter,I., Rotert,S., Saxel,H., Scheer,M., Thiele,S. and Wingender,E. (2003). TRANSFAC®: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.\n11. Kel,A.E., GÖßling,E., Reuter,I., Cheremushkin,E., Kel-Margoulis,O.V. and Wingender,E. (2003) MATCHTM: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.\n12. Chekmenev,D.S., Haid,C. and Kel,A.E. (2005) P-MatchTM: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res., 33, W432-437.\n13. Kel-Margoulis,O., Matys,V., Choi,C., Reuter,I., Krull,M., Potapov,A.P., Voss,N., Liebich,I., Kel,A., and Wingender,E. (2005) Databases on Gene Regulation. In Bajic,V.B. and Tan,T.W. (ed.), Information Processing And Living Systems. World Scientific Publishing Co, Singapore, Vol. 2, pp. 709-727. ",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D108",
"email": "vma@biobase.de"
},
{
"name": "TransfactomeDB",
"url": "http://bussemaker.bio.columbia.edu:8080/YeastTransfactomeDB/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1141",
"desc": "Nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D125",
"email": "hjb2004@columbia.edu"
},
{
"name": "TransmiR",
"url": "http://cmbi.bjmu.edu.cn/transmir",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1343",
"desc": "Regulatory relations between transcription factors and microRNAs",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D119",
"email": "cuiqinghua@hsc.pku.edu.cn"
},
{
"name": "TRANSPATH<sup>®</sup>",
"url": "http://www.gene-regulation.com/pub/databases.html#transpath",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/341",
"desc": "TRANSPATH® is a database on signal transduction pathways that are modeled as bipartite graphs with molecules and reactions as node classes [1,2,3,4,5]. The molecule entries include polypeptides, modified forms, multicomponent complexes, high-order abstractions like families of proteins as well as other molecules such as Ca2+, NO, ATP, H2O. Reaction entries connect molecules, give information on the interaction mechanism and effects and constitute chains and pathways. Individual reactions or chains of subsequent reactions define a direction of signal flow [6]. The integration with TRANSFAC®, a database on transcription factors and their DNA binding sites [7], provides the possibility to present the complete signaling pathways, from extracellular ligands through adaptors and kinase cascades to transcription factors and their target genes. In many cases the protein products of target genes are themselves involved in signal transduction events. Data have been manually extracted from peer-reviewed literature and are curated by experts. The reliability of interaction data in terms of the biological relevance is evaluated and a respective quality value is assigned. Cross-references to important sequence and signature databases such as EMBL/GenBank, UniProt/Swiss-Prot, InterPro, or Ensembl, EntrezGene, RefSeq are provided. The database is equipped with the tools for data visualisation and analysis [1,2,4,5]. The PathwayBuilder™ tool offers four different modes of network visualisation.",
"ref": "1. Schacherer,F., Choi,C., GÖtze,U., Krull,M., Pistor,S. and Wingender,E. (2001) The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics 17, 1053-1057.2. Krull,M., Voss,N., Choi,C., Pistor,S., Potapov,A. and Wingender,E. (2003)TRANSPATH®: an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res., 31, 97-100.3. Wingender, E. (2003) TRANSFAC®, TRANSPATH® and CYTOMER® as starting points for an ontology of regulatory networks. In Silico Biol., 4, 0006. 4. Choi,C., Crass,T., Kel,A., Kel-Margoulis,O., Krull,M., Pistor,S., Potapov,A., Voss,N. and Wingender,E. (2004). Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database. Genome Inform. Ser., 15, 244-254.5. Kel-Margoulis,O., Matys,V., Choi,C., Reuter,I., Krull,M., Potapov,A.P., Voss,N., Liebich,I., Kel,A., and Wingender,E. (2005) Databases on Gene Regulation. In Bajic,V.B. and Tan,T.W. (ed.), Information Processing And Living Systems. World Scientific Publishing Co, Singapore, Vol. 2, pp. 709-727.6. Potapov,A. and Wingender,E. (2001) Modeling the architecture of regulatory networks. In Wingender,E., HofestÄdt,R., Liebich,I. (eds.), Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig, pp. 6-10.7. Matys,V., Fricke,E., Geffers,R., GÖßling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas, D., Kel,A.E., Kel-Margoulis,O.V., Kloos,D.U., Land,S., Lewicki-Potapov,B., Michael,H., MÜnch,R., Reuter,I., Rotert,S., Saxel,H., Scheer,M., Thiele,S., and Wingender,E. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles, Nucleic Acids Res., 31, 374-378.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D546",
"email": "mkl@biobase.de"
},
{
"name": "Transterm",
"url": "http://mrna.otago.ac.nz/Transterm.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/48",
"desc": "Transterm is a database that facilitates studies of translation and the translational control of protein synthesis. It contains a curated collection of motifs in mRNAs that control translation, and also biologically relevant mRNA regions extracted from GenBank. It is organised largely on a taxonomic basis with files and summaries for each species. Global patterns that may affect translation in particular species for example bias in the context of initiation codons (Kozaks consensus, or Shine Dalgarno sequences) or termination codons can be detected in the summary consensus and information content biases summaries. Several types of access are provided via a web browser interface. Transterm defined motifs may be matched in a users sequence or in the database. Alternatively, motifs can be entered by the user to search specific sections of the database (for example coding regions or 3' flanking regions) or the user's sequence. Each Transterm defined motif has an associated biological description with references. The database is accessible at http://uther.otago.ac.nz/Transterm.html",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D72",
"email": "chris.brown@stonebow.otago.ac.nz"
},
{
"name": "TRED - Transcriptional Regulatory Element Database",
"url": "http://rulai.cshl.edu/tred/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/757",
"desc": "Transcriptional regulatory element database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D137",
"email": null
},
{
"name": "TRRD",
"url": "http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/49",
"absurl": null,
"email": null
},
{
"name": "TrSDB",
"url": "http://ibb.uab.es/trsdb/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/314",
"desc": "Transcription factor database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D171",
"email": null
},
{
"name": "UniPROBE",
"url": "http://thebrain.bwh.harvard.edu/pbms/webworks_pub/index.php",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1209",
"desc": "Universal Protein binding microarray Resource for Oligonucleotide Binding Evaluation",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D77",
"email": null
},
{
"name": "VISTA Enhancer Browser",
"url": "http://enhancer.lbl.gov/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/968",
"desc": "Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo.This paucity of enhancer collections with defined activities has thus hindered computational approaches for the genome-wide prediction of enhancers and their functions.To fill this void, we utilize comparative genome analysis to identify candidate enhancer elements in the human genome coupled with the experimental determination of their in vivo enhancer activity in transgenic mice.These data are available through the VISTA Enhancer Browser (http://enhancer.lbl.gov).This growing database currently contains over 250 experimentally tested DNA fragments, of which more than 100 have been validated as tissue-specific enhancers.For each positive enhancer, we provide digital images of whole-mount embryo staining at embryonic day 11.5 and an anatomical description of the reporter gene expression pattern.Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to a particular tissue, or download entire collections of enhancers with a defined tissue specificity or conservation depth.These experimentally validated training sets are expected to provide a basis for a wide range of downstream computational and functional studies of enhancer function.",
"ref": null,
"absurl": null,
"email": "LAPennacchio@lbl.gov"
},
{
"name": "WebGeSTer DB",
"url": "http://pallab.serc.iisc.ernet.in/gester/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1339",
"desc": "Genome Scanner for bacterial transcriptional Terminators",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D129",
"email": "dpal@serc.iisc.ernet.in"
},
{
"name": "YEASTRACT",
"url": "http://www.yeastract.com/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/792",
"desc": "The YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking; http://www.yeastract.com) database is a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. This database is a repository of more than 12000 regulatory associations between transcription factors and target genes, based on experimental evidence which were spread throughout more than 850 bibliographic references. It also includes more than 250 specific DNA binding sites for more than a hundred characterized transcription factors. Further information about each yeast gene included in the database was obtained from Saccharomyces Genome Database (SGD), Regulatory Sequences Analysis Tools (RSAT) and Gene Ontology (GO) Consortium. Computational tools are also provided to facilitate the exploitation of the gathered data when solving a number of biological questions as exemplified in the Tutorial also available on the system. YEASTRACT allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs, such as those found to be over-represented in the promoter regions of co-regulated genes, and the transcription factor binding sites described in the literature. The system also provides an useful mechanism for grouping a list of genes (for instance a set of genes with similar expression profiles as revealed by microarray analysis) based on their regulatory associations with known transcription factors.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D161",
"email": "isacorreia@ist.utl.pt"
},
{
"name": "YeTFaSCo",
"url": "http://yetfasco.ccbr.utoronto.ca/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1462",
"desc": "Yeast Transcription Factor binding Site sequence Collection",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D169",
"email": "carlgdeboer@gmail.com"
},
{
"name": "16S and 23S Ribosomal RNA Mutation Database",
"url": "http://ribosome.fandm.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/229",
"desc": "Access to the expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases has been improved to permit searches of the lists of alterations for all the data from (1) one specific organism, (2) one specific nucleotide position, (3) one specific phenotype, or (4) a particular author. The URL for the searchable version of the Databases is: http://ribosome.fandm.edu. The database currently consists of 1024 records, including 485 16S rRNA records from Escherichia coli, 37 16S-like rRNA records from other organisms, 421 23S rRNA records from E. coli, and 81 23S-like records from other organisms. The numbering of positions in all records corresponds to the numbering in E. coli. We welcome any suggested revisions to the database, as well as information about newly characterized 16S or 23S rRNA mutations.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/26/1/280",
"email": "ktriman@fandm.edu"
},
{
"name": "3D rRNA modification maps",
"url": "http://people.biochem.umass.edu/fournierlab/3dmodmap/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1041",
"desc": "Locations of modified rRNA nucleotides within the 3D structure of the ribosome",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D178",
"email": "mfournie1@gmail.com"
},
{
"name": "5S Ribosomal RNA Database",
"url": "http://biobases.ibch.poznan.pl/5SData/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/230",
"desc": "5S ribosomal RNA is an integral component of the large subunit of all cytoplasmic and most organellar ribosomes. Its small size and association with ribosomal as well as non-ribosomal proteins made it an ideal model RNA molecule for studies of RNA structure and RNA-protein interactions. 5S Ribosomal RNA Database provides information on nucleotide sequences of 5S rRNAs and their genes. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The databaes is available on line at http://biobases.ibch.poznan.pl/5SData/ .",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/30/1/176",
"email": "jbarcisz@ibch.poznan.pl"
},
{
"name": "Aptamer Database",
"url": "http://aptamer.icmb.utexas.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/411",
"desc": "Aptamers are DNA or RNA molecules that have been selected from random pools based on theirability to bind ligands such as small organic or inorganic compounds, peptides, proteins, and even entire organisms. Like antibodies, aptamers have high affinity and specificity for their targets, and thus have many potential uses in medicine and technology. The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection experiments. It is useful not only as a compendium of the research that has been carried out and the sequences that are known, but as a unique resource for theoretical and evolutionary biologists who wish to explore the distribution and relationships between functional nucleic acids. The database is available via the web at http://aptamer.icmb.utexas.edu.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D95",
"email": "aptamer@ellingtonlab.org"
},
{
"name": "ARED",
"url": "http://brp.kfshrc.edu.sa/ARED/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/232",
"desc": "The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenuous agents such as microbes,inflammatory and environmental stimuli. The Adenylate Uridylate (AU)-Rich Element Database, ARED-mRNA version 2.0, contains information not present in the previous ARED. This includes additional data entries , new information and links to Unigene, LocusLink, RefSeq records, and mouse homologue data. An ARE consensus sequence specific to the 3¢UTR is the basis of ARED that demonstrated two important findings: (i) AREs are present in a large, previously unrecognized set of human mRNAs; and (ii) ARE-mRNAs encode proteins of diverse functions which are largely involved in early and transient biological responses. In this update, we have modified the strategy for identifying ARE-mRNA in order to systematically deal with inconsistencies of molecule type and mRNA region in GenBank records. Potential uses for the ARED in functional genomics are also given. The database is accessible via the web, http://rc.kfshrc.edu.sa/ared, with a new querying system that allows searching ARE-mRNAs by any public database identifier or name. The ARED website also contains relevant links to uses for the ARED.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D137",
"email": "khabar@kfshrc.edu.sa"
},
{
"name": "BPS",
"url": "http://bps.rutgers.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1216",
"desc": "Database of RNA Base-Pair Structures",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D83",
"email": null
},
{
"name": "BSRD",
"url": "http://kwanlab.bio.cuhk.edu.hk/BSRD",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1597",
"desc": "BSRD is a resource for bacterial sRNA sequences with extensive annotation and expression profiles. BSRD provides combinatorial regulatory networks of transcription factors and sRNAs with their common targets. There is also a novel RNA-Seq analysis platform, sRNADeep, to characterize sRNAs expression profiles in large-scale transcriptome sequencing projects.",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1264",
"email": "hoishankwan@cuhk.edu.hk"
},
{
"name": "Cereal Small RNA Database",
"url": "http://sundarlab.ucdavis.edu/smrnas/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/982",
"desc": "Small RNAs (smRNAs), which include microRNAs (miRNAs), small-interfering RNAS (siRNAs) and trans-acting siRNAs (ta-siRNAs) are ~19-24 nt RNAs that are important negative regulators of nucleotide sequences involved in development, homeostasis and in the maintenance of heterochromatic states. The Cereals Small RNA Database (CSRDB) is an integrated resource for small RNAs expressed in rice and maize that includes a genome browser and a smRNA-target relational database as well as relevant bioinformatic tools. The resource currently contains a preliminary dataset of 35,454 and 68,871 mapped smRNA sequence reads for rice and maize respectively. Future updates will include smRNA data derived from different tissues and conditions. The database is accessible online at http://sundarlab.ucdavis.edu/smrnas/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D829",
"email": "camjohnson@ucdavis.edu"
},
{
"name": "CORG - A database for COmparative Regulatory Genomics",
"url": "http://corg.molgen.mpg.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/337",
"desc": "Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG - 'COmparative Regulatory Genomics' - database. The data were computed based on statistically significant local suboptimal alignments of 15Kb regions upstream of the translation start sites of, currently, 10,793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service (http://corg.molgen.mpg.de) for query and interactive visualization of the conserved blocks and their annotation.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D32",
"email": "christoph.dieterich@molgen.mpg.de"
},
{
"name": "DARNED",
"url": "http://beamish.ucc.ie/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1673",
"desc": "Database of RNA Editing",
"ref": "1. Kiran A., Baranov P.V. DARNED: a DAtabase of RNa EDiting in humans (2010). Bioinformatics 15;26(14):1772-6. (doi: 10.1093/bioinformatics/btq285).\n",
"absurl": null,
"email": "brave.oval.pan@gmail.com"
},
{
"name": "Database for Bacterial Group II Introns",
"url": "http://www.fp.ucalgary.ca/group2introns/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/378",
"desc": "Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We have initiated an ongoing web site database for mobile group II introns in order to provide correct information on the introns, particularly in bacteria. Information in the web site includes: 1) introductory information on group II introns; 2) detailed information on subfamilies of intron RNA structures and intron-encoded proteins; 3) a listing of identified introns with correct boundaries, RNA secondary structures and other detailed information; and 4) phylogenetic and evolutionary information. The comparative data should facilitate study of the function, spread and evolution of group II introns. The database can be accessed at http://www.fp.ucalgary.ca/group2introns/.",
"ref": "http://dx.doi.org/10.1093/nar/GKR1043",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D187",
"email": "zimmerly@ucalgary.ca"
},
{
"name": "dbRES",
"url": "http://bioinfo.au.tsinghua.edu.cn/dbRES/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/984",
"desc": "Although a large amount of experimentally-derived information about RNA editing sites currently exists, this information has remained scattered in a variety of sources and in diverse data formats. Availability of standard collections for high-quality experimental data will be great helpful for systematic studying of RNA editing, especially for developing computational algorithm to predict RNA editing site. dbRES (http://bioinfo.au.tsinghua.edu.cn/dbRES) is a public database of known RNA editing sites. All sites are manually curated from literature and GenBank annotations. dbRES version 1.1 contains 5437 RNA editing sites of 251 transcripts, covering 96 organisms across plant, metazoan, protozoa, fungi and virus. dbRES provides comprehensive annotations and data summaries, including (but not limited to) transcript sequences, RNA editing types, editing site locations, amino acid changes, organisms, subcellular organelles (if available), cited references, etc. A user-friendly web interface is developed to facilitate both retrieving data and online display of RNA edit site information.",
"ref": "1. Gott, J.M. (2003) Expanding genome capacity via RNA editing. C R Biol, 326, 901-908.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D141",
"email": "daulyd@tsinghua.edu.cn"
},
{
"name": "deepBase",
"url": "http://deepbase.sysu.edu.cn/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1344",
"desc": "A platform for mining and visualization of next generation sequencing data",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D123",
"email": "yjhua2110@yahoo.com.cn"
},
{
"name": "DIANA-LncBase",
"url": "http://www.microrna.gr/LncBase",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1598",
"absurl": "http://dx.doi.org/10.1093/nar/gks1246",
"email": "hatzigeorgiou@fleming.gr"
},
{
"name": "doRiNA",
"url": "http://dorina.mdc-berlin.de/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1463",
"desc": "Database of RNA interactions in post-transcriptional regulation",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D180",
"email": "christoph.dieterich@mdc-berlin.de"
},
{
"name": "European rRNA database",
"url": "http://www.psb.ugent.be/rRNA/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/463",
"desc": "All complete or nearly complete rRNA sequences",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D101",
"email": null
},
{
"name": "FlyRNAi",
"url": "http://flyrnai.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/817",
"absurl": null,
"email": null
},
{
"name": "fRNAdb",
"url": "http://www.ncrna.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1027",
"desc": "Functional RNA Database (fRNAdb) is a database service that hosts a large collection of non-coding transcripts including annotated/un-annotated sequences from H-inv database, NONCODE, and RNAdb. A set of computational sequence analyses are performed over these registered sequences. The analyses include RNA secondary structure motif discovery, EST support, finding cis-regulatory elements, sequence homology search, etc. The fRNAdb provides an efficient interface to help users filter out particular transcripts that match their own criteria to sort out functional RNA candidates.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D89",
"email": null
},
{
"name": "Greengenes",
"url": "http://greengenes.lbl.gov/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/878",
"desc": "An online full-length small-subunit (SSU) rRNA gene database called 'greengenes' that keeps pace with public submissions of both archaeal and bacterial 16S rDNA sequences has been established. It addresses a number of limitations currently associated with SSU rRNA records in the public databases by providing automated chimera-screening, taxonomic placement of unclassified environmental sequences using multiple published taxonomies for each record, multiple standard alignments and uniform sequence-associated information curated from GenBank records. Manipulation of 72,918 rDNA records revealed putative chimeras in 5% (1,901 of 38,412) of environmental sequences and, surprisingly, 0.5% (201/36,643) of records derived from isolates.Greengenes also provides a suite of utensils for manipulation of sequences including an alignment tool and has been streamlined to interface with the widely used ARB program.",
"ref": "1. DeSantis, T.Z., Dubosarskiy, I., Murray, S.R., and Andersen, G.L. (2003) Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. Bioinformatics 19(12), 1461-1468.",
"absurl": "",
"email": "glandersen@lbl.gov"
},
{
"name": "GRSDB",
"url": "http://bioinformatics.ramapo.edu/GRSDB2/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/820",
"desc": "GRSDB: ‘G’-Rich Sequences DataBase contains information on composition and distribution of putative Quadruplex forming 'G'-Rich Sequences (QGRS) in the alternatively processed (alternatively spliced or alternatively polyadenylated) mammalian pre-mRNA sequences. The data stored in the GRSDB is based on computational analysis of genomic nucleotide sequences obtained from fully annotated GenBank/RefSeq entries that provide alternative processing information. In addition to providing data on composition and locations of QGRS relative to the processing sites in the pre-mRNA sequence, GRSDB features visual comparison of QGRS distribution patterns among all the alternative RNA products of a gene with the help of dynamically generated graphics. . GRSDB can be accessed at http://bioinformatics.ramapo.edu/grsdb/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D141",
"email": "pbagga@ramapo.edu"
},
{
"name": "GtRDB - Genomic tRNA Database",
"url": "http://gtrnadb.ucsc.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/490",
"absurl": null,
"email": null
},
{
"name": "HIV Sequence Database",
"url": "http://www.hiv.lanl.gov/content/index",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/76",
"desc": "The HIV Sequence Database contains all published and many unpublished HIV and related SIV DNA and translated amino acid sequences. Currently, >95,000 entries are maintained and annotated. The database is fully searchable through several search tools and contains many tools for sequence analysis.The search tools include an interface where sequences are searchable through accession number, name, sampling country, subtype, sampling year, risk factor, coreceptor usage, phenotype and more. Another search tool uses geographic subtype distributions. The search results are presented as tables covering important sequence information and the sequences can be downloaded as multiple pairwise alignments. Some examples among the many tools are: Gene Cutter that clips pre-defined coding regions from a nucleotide alignment, then codon aligns and provides translations of the cut regions, Seq-Covert that converts between different formats, Primalign that aligns your primer or sequence fragment to the complete genome alignment, the HIV/SIV Sequence Locator that finds the position of your nucleotide or protein sequence in HIV relative to a reference, RIP that performs a recombination analysis, Hypermut that can detect hypermutated sequences, SNAP that calculates synonymous and non-synonymous substitutions, PCoord that summarizes variation among sequences in ten 'dimensions' where each sequence gets a score on each of these dimensions, and HIV-BLAST that performs a BLAST search on HIV sequences. Some simple tree building interfaces are present and more advanced and versatile tree tools are currently being developed.The database also provides alignments of all full length HIV and SIV genomes, consensus and reconstructed ancestral sequences, and reference sequences for subtyping, recombination analyses and other purposes.In addition, the database publishes a yearly hard copy compendium with selected sequences and review articles on recent developments in HIV genetic research. These reviews and additional tutorials on sequence analysis are also available on the web site.",
"ref": null,
"absurl": "",
"email": "tkl@lanl.gov"
},
{
"name": "HMDD v2.0 - Human microRNA Disease Database version 2.0",
"url": "http://cmbi.bjmu.edu.cn/hmdd",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1680",
"desc": "The HMDD database is a collection of experimentally supported human microRNA (miRNA) and disease associations. Here, we describe the HMDD v2.0 update that presented several novel options for users to facilitate exploration of the data in the database.By keeping datasets up-to-date, HMDD should continue to serve as a valuable resource for investigating the roles of miRNAs in human disease.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D1070",
"email": "cuiqinghua@bjmu.edu.cn"
},
{
"name": "HuSiDa - Human siRNA database",
"url": "http://itb.biologie.hu-berlin.de/~nebulus/sirna/index.htm",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/689",
"desc": "Human siRNA database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D108",
"email": null
},
{
"name": "IRESdb - the Internal Ribosome Entry Site database",
"url": "http://ifr31w3.toulouse.inserm.fr/IRESdatabase/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/379",
"desc": "Internal Ribosome Entry Sites (IRES) are cis-acting RNA sequences able to mediate internal entry of the 40S ribosomal subunit on some eukaryotic and viral messenger RNAs upstream of a translation initiation codon. These sequences are very diverse and are present in a growing list of mRNAs. Novel IRES sequences continue to be added to public databases every year and the list of unknown IRESes is certainly still very large. The IRES database is a comprehensive WWW ressource for internal ribosome entry sites and presents currently available general informations as well as detailed data for each IRES. It is a searchable, periodically updated collection of IRES RNA sequences. Sequences are presented in FASTA form and hotlinked to NCBI GenBank files. Several subsets of data are classified according to the viral taxon (for viral IRESes), to the gene product function (for cellular IRESes), to the possible cellular regulation or to the trans-acting factor that mediates IRES function. This database is accessible at http://ifr31w3.toulouse.inserm.fr/IRESdatabase/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/31/1/427",
"email": "vagner@toulouse.inserm.fr"
},
{
"name": "IRESite",
"url": "http://www.iresite.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/831",
"desc": "IRESite is a searchable collection of data concerning the Internal Ribosome Entry Segments (IRES) both of viral and cellular origin. IRESs are the RNA regions which are mostly defined functionally by their ability to attract a eukaryotic ribosomal translation initiation complex independently of presence of the commonly utilized 5'-terminal 7mG cap structure and thus to promote translation initiation even at the internal part of the RNA molecule.IRESite can provide a broad set of information referring to particular IRES - briefly: primary sequence data, functional data, RNA structure and possible ribosomal RNA complementarity data, RNA:protein interaction data, links to primary databases, information about the relevant experiments and more. Most of the data are not available in the primary databases and are manually extracted from literature sources by IRESite curators. New data can also be submitted through the publicly available IRESite web interface after creating a personal account, however their release needs the curators' approval.Brief graphical overview of the database is present at http://www.iresite.org/docs/iresite.pdf",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D131",
"email": "martin@natur.cuni.cz"
},
{
"name": "ITS2",
"url": "http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?about",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1090",
"desc": "Predicted structures of internal transcribed spacer 2 (ITS2)",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D275",
"email": "Joerg.Schultz@biozentrum.uni-wuerzburg.de"
},
{
"name": "Lncipedia",
"url": "http://www.lncipedia.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1599",
"desc": "Human lncRNA gene sequences and structures",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks915",
"email": "PieterJan.Volders@ugent.be"
},
{
"name": "lncRNAdb",
"url": "http://www.lncrnadb.com/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1420",
"desc": "Long Non-Coding RNA Database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D146",
"email": "http://www.lncrnadb.com/SubmitNew.aspx"
},
{
"name": "MeRNA",
"url": "http://merna.lbl.gov/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/838",
"desc": "MeRNA (Metals in RNA) is a comprehensive compilation of all metal binding sites identified in RNA three-dimensional structures available from the Protein Data Bank (PDB) and Nucleic Acid Database. Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements; in 256 RNA structures with coordinates released before July 1, 2005. MeRNA includes eight manually identified metal-ion binding motifs, which are described in the literature.MeRNA is searchable by PDB identifier, metal ion, method of structure determination, resolution and R-values for X-ray structure, and distance from metal to any RNA atom or to water.New structures with their respective binding motifs will be added to the database as they become available. The MeRNA database is accessible at http://merna.lbl.gov.",
"ref": "Stefan LR, Zhang R, Levitan AG, Hendrix DK, Brenner SE, Holbrook SR. (2006) MeRNA: a database of metal ion binding sites in RNA structures. Nucleic Acids Res. 34: in press.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D131",
"email": "SRHolbrook@lbl.gov"
},
{
"name": "mESAdb",
"url": "http://konulab.fen.bilkent.edu.tr/mirna/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1455",
"desc": "microRNA Expression and Sequence Analysis Database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D170",
"email": "konu@fen.bilikent.edu.tr"
},
{
"name": "microRNA.org",
"url": "http://www.microrna.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1097",
"desc": "microRNA target predictions and expression profiles",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D149",
"email": "betel@cbio.mskcc.org"
},
{
"name": "miR2Disease",
"url": "http://www.mir2disease.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1234",
"desc": "Literature-curated database for validatedly or potentially pathogenic roles of dysregulated miRNAs in human disease",
"ref": "Jiang Q., Wang Y., Hao Y., Juan L., Teng M., Zhang X., Li M., Wang G., Liu Y., (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37:D98-104.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D98",
"email": "yunliu@iupui.edu"
},
{
"name": "miRBase",
"url": "http://www.mirbase.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/529",
"desc": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. The miRBase Registry continues to provide gene hunters with unique names for novel miRNA genes prior to publication of results. The miRBase Targets database is a new resource of predicted miRNA targets in animals",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D68",
"email": "sam.griffiths-jones@manchester.ac.uk"
},
{
"name": "miRecords",
"url": "http://mirecords.umn.edu/miRecords/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1278",
"desc": "Experimentally validated miRNAs",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D105",
"email": null
},
{
"name": "miREX",
"url": "http://bioinfo.amu.edu.pl/mirex",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1464",
"desc": "Plant microRNA Expression data",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D191",
"email": "wojciech.karlowski@amu.edu.pl"
},
{
"name": "miRGator",
"url": "http://genome.ewha.ac.kr/miRGator/miRGator.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1098",
"desc": "microRNA target prediction, functional analysis, and gene expression data",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D159",
"email": "sanghyuk@ewha.ac.kr"
},
{
"name": "miRGen",
"url": "http://www.diana.pcbi.upenn.edu/miRGen/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/994",
"desc": "miRGen is an integrated database of (1) positional relationships between animal miRNAs and genomic annotation sets, and (2) mammalian miRNA targets according to combinations of widely used target prediction programs.A major goal of the database is the study of the relationship between miRNA genomic organization and miRNA function.This is made possible by three integrated and user friendly interfaces.The Genomics interface allows the user to explore where whole-genome collections of miRNAs are located with respect to UCSC genome browser annotation sets such as Known Genes, Refseq Genes, Genscan predicted genes, CpG islands, and pseudogenes.These miRNAs are connected through the Targets interface to their experimentally supported target genes from TarBase, as well as computationally predicted target genes from optimized intersections and unions of several widely used mammalian target prediction programs.Finally, the Clusters interface provides predicted miRNA clusters at any given inter-miRNA distance, and provides specific functional information on the targets of miRNAs within each cluster.All of these unique features of miRGen are designed to facilitate investigations into miRNA genomic organization, co-transcription, and targeting.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D149",
"email": "megraw@mail.med.upenn.edu"
},
{
"name": "miRNAMap",
"url": "http://mirnamap.mbc.nctu.edu.tw/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/895",
"desc": "microRNA precursors and their mapping to targets in vertebrate genomes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D165",
"email": "bryan@mail.nctu.edu.tw"
},
{
"name": "miRNEST",
"url": "http://mirnest.amu.edu.pl/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1465",
"desc": "microRNAs in animal and plant EST sequences",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D74",
"email": "szczesniak.pl@gmail.com"
},
{
"name": "miROrtho",
"url": "http://cegg.unige.ch/mirortho/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1232",
"desc": "Computational prediction of animal microRNA genes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D111",
"email": null
},
{
"name": "miRTarBase",
"url": "http://mirtarbase.mbc.nctu.edu.tw/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1423",
"desc": "Experimentally validated microRNA-target interactions",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D78",
"email": "bryan@mail.nctu.edu.tw"
},
{
"name": "MODOMICS",
"url": "http://genesilico.pl/modomics/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/840",
"desc": "MODOMICS ('omics' approach to RNA modification) integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions. MODOMICS also provides literature information, and links to other databases, including the available protein sequence and structure data. MODOMICS can be queried by the type of nucleoside, type of RNA, position of a particular nucleoside, type of reaction (e.g. methylation, thiolation, deamination, etc.), and name or sequence of an enzyme of interest. The contents of MODOMICS can be accessed through the World Wide Web at http://genesilico.pl/modomics/.",
"ref": "1. Bujnicki, J.M., Droogmans, L., Grosjean, H., Purushothaman, S.K., Lapeyre, B. (2004) Bioinformatics-guided identification and experimental characterization of novel RNA methyltransferases. In Nucleic Acids and Molecular Biology series, \"Practical Bioinformatics\". Editor: Bujnicki, J.M. Springer-Verlag\n2. Dunin-Horkawicz, S., Czerwoniec, A., Gajda, M.J., Feder, M., Grosjean, H., and Bujnicki, J.M. (2006) MODOMICS: a database of RNA modification pathways. Nucleic Acids Res. 34, D145-9\n3. Czerwoniec, A., Dunin-Horkawicz, S., Purta, E., Kaminska, K.H., Kasprzak, J.M., Bujnicki, J.M.,Grosjean, H., and Rother, K. (2009) MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res. 37, D118-21",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D118",
"email": "iamb@genesilico.pl"
},
{
"name": "NAPP",
"url": "http://rna.igmors.u-psud.fr/NAPP",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1466",
"desc": "Nucleic Acid Phylogenetic Profile database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/40/D1/D205",
"email": "daniel.gautheret@u-psud.fr"
},
{
"name": "NATsDB",
"url": "http://natsdb.cbi.pku.edu.cn/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/997",
"desc": "Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense partners. They regulate sense genes at multiple levels and are implicated in various diseases. Using an improved whole-genome computational pipeline, we identified abundantcis-encoded exon-overlapping sense-antisense (SA) gene pairs in human,mouse, fly, and eight other eukaryotic species. We developed NATsDB (Natural Antisense Transcripts DataBase, http://natsdb.cbi.pku.edu.cn/)to enable efficient browsing, searching and downloading of this currently mostcomprehensive collection of SA genes, grouped into six classes based on theiroverlapping patterns.NATsDB also includes Non-exon-Overlapping Bidirectional (NOB) genesand Non-BiDirectional (NBD) genes.To facilitate the study of functions, regulations, andpossible pathological implications, NATsDB includes extensive information about genestructures, polyA signals and tails, phastCons conservation, homologues in other species,repeat elements, EST expression profiles, and OMIM disease association.NATsDB supports interactive graphical display of the alignment of all supporting ESTand mRNA transcripts of the SA and NOB genes to the genomic loci.It supports advancedsearch by species, gene name, sequence accession number, chromosome location, codingpotential, OMIM association, and sequence similarity.",
"ref": "1.Zhang, Y., Li, J., Kong L., Gao, G., Liu QR., and Wei L. (2007)NATsDB: Natural Antisense Transcripts DataBase. Nucleic Acids Res. 35, in press",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D156",
"email": "weilp@mail.cbi.pku.edu.cn"
},
{
"name": "NCIR - Non-Canonical Interactions in RNA",
"url": "http://prion.bchs.uh.edu/bp_type/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/380",
"desc": "The known occurrences of non-canonical base-base interactions in RNA are tabulated in the NCIR (http://prion.bchs.uh.edu/bp_type/) database. Currently, there are over 1700 entries including those from the crystal and NMR structures of RNAs published in the year 2003/2004. The database summarizes the important structural properties of these interactions such as the sequence context, the sugar pucker, glycosidic conformation, melting temperature, chemical shift and free energy, when the information is available. The recent nomenclature proposed by Leontis and Westhof (1) has been incorporated into the database based on the three interacting edges: Watson-Crick (WC), Hoogsteen (HG), sugar edge (SE). To date, 46 different base pairs connected by at least two hydrogen bonds have been observed. Additionally, base pairs connected by single and bifurcated hydrogen bonds are also observed. Higher order base-base interactions including base triples, quadruples and quintuples have also been categorized. Frequently occurring non-canonical base pairs are the GA trans SE/HG, AU trans HG/WC, GA cis WC/WC, UU cis WC/SE and the GU and the AC cis wobble pairs. The most common base triple is an AGC trans SE/SEcis WC/WC interaction, often stabilizing long range tertiary interaction in RNA. A recent addition to the entries includes RNA motif information for the associated base-base interactions.",
"ref": "1. Leontis,N.B. and Westhof,E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA,7,499-512.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/30/1/395",
"email": "fox@uh.edu"
},
{
"name": "ncRNAs database",
"url": "http://biobases.ibch.poznan.pl/ncRNA/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/381",
"desc": "The noncoding RNAs database is a colection of currently available sequence data on RNAs, which do not have protein-coding capacity and have been implicated in regulation of cellular processes. The RNAs included in the database form very heterogenous group of molecules that cat on different levels of information transmission in the cell. It includes RNAs acting on the level of chromatin structure, throug transcriptional and translational regulation of gene expression to modulation of protein function and regulation of subcellular distribution of RNAs and proteins. Some of these RNAs have been shown to be connected with developmental disorders in humans. In recent years RNAs with potential regulatory functions have been found in prokaryotic, animal and plant cells. Currently the database contains over 100 sequences of noncoding RNAs and can be accessed via WWW at http://biobases.ibch.poznan.pl/ncRNA/ .",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D162",
"email": "jbarcisz@ibch.poznan.pl"
},
{
"name": "NONCODE",
"url": "http://noncode.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/705",
"desc": "A database of noncoding RNAs",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D98",
"email": "biozy@ict.ac.cn"
},
{
"name": "NPInter",
"url": "http://www.bioinfo.org.cn/NPInter/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/845",
"desc": "The Noncoding RNAs and Protein related biomacromolecules Interaction database (NPInter; http://bioinfo.ibp.ac.cn/NPInter or http://www.bioinfo.org.cn/NPInter) is a database that documents experimentally determined functional interactions between noncoding RNAs (ncRNAs) and protein related biomacromolecules (proteins, mRNAs or genomic DNAs). NPInter intends to provide the scientific community with a comprehensive and integrated tool for efficient browsing and extraction of information on interactions between ncRNAs and protein related biomacromolecules (PRMs). Beyond cataloguing details of these interactions, the NPInter will be useful for understanding ncRNA function, as it adds a very important functional element – noncoding RNAs - to the biomolecule interaction network and sets up a bridge between the coding and the noncoding kingdoms.By functional interactions we mean both physical interactions between an ncRNA and a protein, and other forms of interaction where the combination of an ncRNA and an mRNA or a genomic DNA sequence elicits a cellular reaction. Although biological knowledge on this sort of interactions is contained in the scientific literature, retrieving it will be much easier with the NPInter database.\nThe database now contains 700 published functional interactions from six model organisms - Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens. The amount of data is not large, but the NPInter covers almost all experimentally verified functional interactions between ncRNA and PRM published before the end of the year 2004.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D104",
"email": "biozy@ict.ac.cn"
},
{
"name": "NRED",
"url": "http://jsm-research.imb.uq.edu.au/nred/cgi-bin/ncrnadb.pl",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1195",
"desc": "Noncoding RNA Expression Database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D122",
"email": null
},
{
"name": "piRNABank",
"url": "http://pirnabank.ibab.ac.in/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1114",
"desc": "Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D173",
"email": "shipra@ibab.ac.in"
},
{
"name": "Plant snoRNA DB",
"url": "http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/564",
"desc": "snoRNA genes in plant species",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/31/1/432",
"email": null
},
{
"name": "PlantRNA",
"url": "http://plantrna.ibmp.cnrs.fr/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1578",
"desc": "The PlantRNA database compiles 4,375 tRNA gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. To the manually curated lists of tRNA genes that we recently extracted from the genomes of five angiosperms (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula, Brachypodium distachyon) and one green alga (Chlamydomonas reinhardtii) (1), we retrieved tRNA genes from the genomes of 6 other photosynthetic organisms, namely another green alga (Ostreococcus tauri), a glaucophyte (Cyanophora paradoxa), a brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum).Whole genomes were scanned by tRNAscan-SE (2) and then manually annotated as described in (1). For each tRNA gene, the linear secondary structure is given as well as biological information. This includes 5'- and 3'- flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Due to the importance of the dual-targeting phenomenon for proteins involved in translation in plants (3), we also put strong effort in providing the subcellular localization of these enzymes. Finally, data on mitochondrial import (3) of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA binding proteins are also included. Transfer RNA gene sequences and optional information can be downloaded in xls or FASTA file formats. In addition, a SQL dump of the database is available upon request.",
"ref": "1.\tMichaud, M., Cognat, V., Duchêne, A.M. and Maréchal-Drouard, L. (2011) A global picture of tRNA genes in plant genomes. Plant J, 66, 80-93.\n",
"absurl": null,
"email": "laurence.drouard@ibmp-cnrs.unistra.fr"
},
{
"name": "PmiRKB",
"url": "http://bis.zju.edu.cn/pmirkb/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1326",
"desc": "Plant microRNA knowledge base",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D181",
"email": "mchen@zju.edu.cn"
},
{
"name": "PolyA_DB",
"url": "http://exon.umdnj.edu/lab_home/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/723",
"desc": "A database of mammalian mRNA polyadenylation",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D165",
"email": null
},
{
"name": "PseudoBase",
"url": "http://pseudobaseplusplus.utep.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/242",
"desc": "PseudoBase is a database containing structural, functional and sequence data related to RNA pseudoknots. It can be reached by its central page at http://pseudobaseplusplus.utep.edu. From here one can retrieve pseudoknot data as well as submit data for pseudoknots that are not yet in the database. There are various alternatives to retrieve data, e.g. in a survey sorted alphabetically on organism names, or sorted on types of RNA molecules or on structural features (such as sizes of paired regions and loops). For each pseudoknot, thirteen items are stored: a PKB-number (a unique number for each pseudoknot entry), definition, organism, abbreviation, category (one of 13 alternatives), keywords, EMBL accession number of the sequence containing this pseudoknot, name of person that submitted the data, support that can be given regarding the reliability of the pseudoknot, reference(s) to relevant paper(s), sizes of each stem, sizes of each loop, the stem positions in the sequence, and finally a so-called bracket view that shows the base-pairs in the pseudoknotted region of the sequence. At the time of writing the database contains over 300 entries with classical H-type pseudoknots as well as more complicated ones.",
"ref": "1. van Batenburg, F.H.D., Gultyaev, A.P., and Pleij, C.W.A.(2001) PseudoBase: structural information on RNA pseudoknots. Nucleic Acids Res., 29(1), 194-195.2. van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A., Ng, J., and Oliehoek, J. (2000) PseudoBase: a database with RNA pseudoknots. Nucleic Acids Res., 28, 201-204.3. Taufer, M., Licon, A., Araiza, R., Mireles, D., van Batenburg, F.H.D., Gultyaev, A.P., and Leung, M.-Y. (2008) PseudoBase++: An Extension of PseudoBase for Easy Searching, Formatting, and Visualization of Pseudoknots, Nucleic Acids Res., 37, D127-D135.",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D127",
"email": "F.H.D.van.Batenburg@biology.leidenuniv.nl"
},
{
"name": "RADAR",
"url": "http://rnaedit.com/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1681",
"desc": "A Rigorously Annotated Database of A-to-I RNA editing",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D109",
"email": "gokulr@stanford.edu"
},
{
"name": "REDIdb",
"url": "http://biologia.unical.it/py_script/search.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1009",
"desc": "An RNA editing database",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D173",
"email": "c.quagliariello@unical.it"
},
{
"name": "RepTar",
"url": "http://reptar.ekmd.huji.ac.il/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1442",
"desc": "Predicted targets of host and viral miRNAs",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/39/suppl_1/D188",
"email": "reptar.adm@ekmd.huji.ac.il"
},
{
"name": "Rfam",
"url": "http://rfam.sanger.ac.uk/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/382",
"desc": "Rfam is a collection of multiple sequence alignments and covariance models representing non-coding RNA families. Rfam is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ and in the US at http://rfam.wustl.edu/. These websites allow the user to search a query sequence against a library of covariance models, and view multiple sequence alignments and family annotation. The database can also be downloaded in flatfile form and searched locally using the INFERNAL package (http://infernal.wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D136",
"email": "pg5@sanger.ac.uk"
},
{
"name": "Ribosomal Database Project (RDP-II)",
"url": "http://rdp.cme.msu.edu/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/243",
"absurl": null,
"email": null
},
{
"name": "RISSC - Ribosomal Internal Spacer Sequence Collection",
"url": "http://egg.umh.es/rissc/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/244",
"desc": "This is a database of ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics. It compiles more than 2500 entries of edited DNA sequence data from the 16S-23S ribosomal spacers present in most prokaryotes and organelles. Ribosomal spacers have proven to be extremely useful tools for typing and identifying closely related prokaryotes due to their high variability in size and/or sequence, much more so than the flanking 16S and 23S rRNA genes. These genes are commonly used to establish molecular relationships among microbes at a taxonomic level of species or higher (e.g genus, domain). However their internal transcribed spacers (ITS) are much more useful to discriminate at the species or even strain level. Currently, many published papers are showing the growing importance of these regions of the ribosomal operon in these types of studies. By creating RISSC, our intention is to provide the scientific community with a comprehensive set of ribosomal spacer sequences, fully edited and characterized with a key feature as is the presence/absence of tRNA genes within them, ready to be used and compared with their own ITS sequences. A second, much shorter, ribosomal spacer can be found between rRNA genes 23S and 5S, also of phylogenetic interest. We intend to incorporate them into the database in the near future.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/29/1/178",
"email": "frvalera@umh.es"
},
{
"name": "RNA FRABASE",
"url": "http://rnafrabase.ibch.poznan.pl/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1129",
"desc": "A database of 3D RNA fragments within known RNA structures",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D386",
"email": "adamiakr@ibch.poznan.pl"
},
{
"name": "RNA Modification Database",
"url": "http://rna-mdb.cas.albany.edu/RNAmods/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/245",
"desc": "Naturally modified nucleosides in RNA",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/27/1/196",
"email": "pamela.crain@rna.pharm.utah.edu"
},
{
"name": "RNA SSTRAND",
"url": "http://www.rnasoft.ca/sstrand/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/900",
"desc": "RNA SSTRAND contains known secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database.",
"ref": null,
"absurl": "",
"email": "hoos@cs.ubc.ca"
},
{
"name": "RNAdb",
"url": "http://research.imb.uq.edu.au/RNAdb/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/630",
"absurl": null,
"email": null
},
{
"name": "RNAi codex",
"url": "http://codex.cshl.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/862",
"desc": "RNAi Codex consists of a database of shRNA related information and an associated website. It has been developed as a portal for publicly available short-hairpin RNA (shRNA) resources and is accessible at http://codex.cshl.org.RNAi Codex currently holds data from the Hannon-Elledge shRNA library and allows the use of biologist-friendly gene names to access information on shRNA constructs that can silence the gene of interest. It is designed to hold user-contributed annotations and publications for each construct, as and when such data become available. RNAi Codex relies upon GeneSeer (http://geneseer.cshl.org) to handle gene names and has a variety of mapping information on genes, coding sequences and the location of the target sequences on the mRNA.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D153",
"email": "sachidan@cshl.org"
},
{
"name": "RNAJunction",
"url": "http://rnajunction.abcc.ncifcrf.gov/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1130",
"desc": "RNA structural elements: helical junctions, internal loops, bulges and loop-loop interactions",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D392",
"email": "bshapiro@ncifcrf.gov"
},
{
"name": "SELEXdb",
"url": "http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/246",
"desc": "SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for these oligomers recognition. In vitro selection of oligomers binding target proteins is a novel technology intensively being developed during the last decade, for sieving a pool of synthetic oligomers through repeated cycles of PCR-amplification and protein-binding selection (1). According to Human Genome Annotation, we have developed the SELEX_DB database on oligomers selected in vitro, the database being supplied by Web-available applets for site recognition (2). Besides, since many disease may be caused not only by the mutation-altered transcription factor binding true-site on DNA, but also by the appearance of a novel protein-fitting noise-site altering a normal regulation of a gene network (e.g., the substitution -376G>A in human TNF gene promoter produces the transcription factor OCT-fitting noise-site causing the clinical phenotype 'severe malaria' (3)), the in vitro selected aptamers are very informative for the Single Nucleotide Polymorphism (SNP) analysis. At the same time, in prokaryota, the discrepancies between in vitro selected and natural sites by nucleotide-position frequency matrices have been comprehensively demonstrated (4). Besides, the positional Information Content matrices of the in vitro selected aptamers was found to be correlating with the protein-binding strength magnitudes, whereas neither correlation was found for the corresponding natural site (5). This means that, in prokaryota, natural sites were selected in vivo according to their biological activity, but not by protein affinity. In eukaryota, the relationship between in vivo and in vitro selections seems to be very knotty. From one hand, the in vitro selected TBP-binding DNAs provide the natural TATA-box activity (6). Moreover, homologous c-Myb and v-Myb proteins, minimal Myb/DNA-binding domain and, Myb-fortified cell nuclear extract are selecting in vitro the aptamers, similarities of which to one the others and to the natural c-Myb sites are significant (7). From the other hand, in vitro selected YY1-binding DNAs, inserted into the plasmids and transfected into various cells ('plasmid+cell' system), repress the reported gene (8), thus supporting the fact that YY1 binding strength and repression magnitudes do not correlate. Moreover, for these in vitro selected YY1-fitting aptamers, these YY1-caused repression measured in vivo at one 'plasmid+cell' system do not correlate to the proper magnitudes detected in vivo at the other 'plasmid+cell' system. According to this evident system-dependence of both in vitro and in vivo selected experimental data, nowadays a fundamental question is how in vitro selected data could be implemented for natural gene analysis (1). That is why novel release of the SELEX_DB has been supported by two databases SYSTEM (9, 10) and CROSS_TEST, storing both experiment systems and their cross-validation tests. By cross-validation testing, we have unexpectedly observed that, for a fixed protein-binding site, the recognition accuracy increases with the growth of homology between the target and test proteins. For natural sites, the recognition accuracy was less than for the nearest protein homologs and higher than for the distant homologs and non-homologous proteins binding the common site. The current SELEX_DB release is available at URL=http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/.",
"ref": null,
"absurl": null,
"email": "jpon@bionet.nsc.ru"
},
{
"name": "siRecords",
"url": "http://sirecords.biolead.org/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1162",
"desc": "Experimentally tested mammalian siRNAs",
"ref": null,
"absurl": "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/8/1027",
"email": "toli@biocompute.umn.edu"
},
{
"name": "siRNAdb",
"url": "http://sirna.sbc.su.se/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/629",
"desc": "The siRNA database provides a gene-centric view of human siRNA experimental data, including siRNAs of known efficacy and siRNAs predicted to be of high efficacy by siSearch. Linked to these sequences is information including siRNA thermodynamic properties and the potential for sequence specific off-target effects. The database provides the user with sufficient data to evaluate the siRNAs potential inhibition and sequence-specific off target effects.In release 1.0 there are 405 experimentally verified siRNAs targeting 50 genes, an average of 8 siRNAs/gene. It contains records and siRNA predictions for all genes in the REFSEQ curated human sequence set (20,410 \"NM\" sequences and 6767 \"XM\" sequences). The database is available at http://sirna.sbc.su.se.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/33/suppl_1/D131",
"email": "alistair.chalk@cgb.ki.se"
},
{
"name": "Sno/scaRNAbase",
"url": "http://bioinfo.fudan.edu.cn/snoRNAbase.nsf",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/962",
"desc": "Sno/scaRNA database (sno/scaRNAbase, http://bioinfo.fudan.edu.cn/snoRNAbase.nsf) was developed to facilitate the research of small nucleolar RNAs (snoRNAs) and cajal body-specific RNAs (scaRNAs) that have been found to play important roles in rRNA, tRNA, snRNA and even mRNA biogenesis. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase currently contains 1,979 sno/scaRNAs records obtained from 85 organisms. It provides an easy-to-use gateway to important sno/scaRNAs features such as conserved sequence motifs and antisense elements of sno/scaRNA families, methylation or pseudouridylationsites that a sno/scaRNA guides, homologues, predicted secondary structures, genomics organizations, sno/scaRNA genes, chromosome locations, functions that are experimentally verified or predicted, etc. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. This sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research.",
"ref": null,
"absurl": null,
"email": "xiejun@fudan.edu.cn"
},
{
"name": "snOPY",
"url": "http://snoopy.med.miyazaki-u.ac.jp/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1750",
"absurl": "http://dx.doi.org/10.1093/nar/",
"email": "kenmochi@med.miyazaki-u.ac.jp"
},
{
"name": "snoRNA-LBME-db",
"url": "http://www-snorna.biotoul.fr/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/869",
"desc": "snoRNA-LBME-db is a collection of human small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs), that serve to guide modifications in rRNAs or snRNAs. The database can be search by sno/scaRNA name or Accession number, or by the position of the modified nucleotide in rRNA/snRNA sequence. Each sno/scaRNA entry is directly linked to the corresponding position at the human UCSC Genome Browser. The database is available on the web at http://www-snorna.biotoul.fr/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D158",
"email": "weber@ibcg.boiotoul.fr"
},
{
"name": "SomamiR",
"url": "http://compbio.uthsc.edu/SomamiR/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1600",
"desc": "Somatic mutations that impact microRNA targeting in cancer",
"ref": null,
"absurl": "http://dx.doi.org/10.1093/nar/gks1138",
"email": "ycui2@uthsc.edu"
},
{
"name": "sRNAMap",
"url": "http://srnamap.mbc.nctu.edu.tw/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1279",
"desc": "small regulatory RNA in microbial genomes",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl_1/D150",
"email": null
},
{
"name": "SRPDB",
"url": "http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/248",
"desc": "Signal recognition particle (SRP) is an ribonucleoprotein particle designed to recognize secretory signal sequences as they emerge from the ribosome. SRP associates with the SRP-receptor in the ER membrane, is released from the ribosome, and recycled (for review, see [1, 2]). To assist the understanding of the molecular details of this essential cellular function, the SRP database (SRPDB) provides sequences of SRP RNAs, SRP proteins, and the SRP receptor ordered alphabetically and phylogenetically with links to the primary sources, as well as a manually-checked alignments. The SRP RNA alignment serves to derive supported secondary structures and helps to evaluate potential tertiary interactions. SRPDB is maintained at the University of Texas Health Science Center at Tyler, Texas, accessible on the World Wide Web at the URL http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and at the European mirror at the University of Goteborg, Sweden (http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html). A web interface is available where a nucleotide sequence can be submitted to predict SRP RNA genes.",
"ref": "[1] Nagai K, Oubridge C, Kuglstatter A, Menichelli E, Isel C, Jovine L. (2003). Structure, function and evolution of the signal recognition particle. EMBO J. 22:3479-3485.[2] Doudna JA, Batey RT. (2004). Structural insights into the signal recognition particle. Annu. Rev. Biochem. 73:539-557.[3] Rosenblad MA, Zwieb C, Samuelsson T. (2004). Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi. BMC Genomics 5:5.[4] Van Nues RW, Brown JD. (2004). Saccharomyces SRP RNA secondary structures: A conserved S-domain and extended Alu-domain. RNA 10:75-89.\n[5] Rosenblad, M.A., Larsen, N., Samuelsson, T., and Zwieb, C. (2009) Kinship in the SRP RNA family. RNA Biol. 6, 508-516",
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D163",
"email": "zwieb@uthscsa.edu"
},
{
"name": "StarBASE",
"url": "http://starbase.sysu.edu.cn/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/1447",
"desc": "microRNA-mRNA interaction maps",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/42/D1/D92",
"email": "lssqlh@mail.sysu.edu.cn"
},
{
"name": "Subviral RNA Database",
"url": "http://subviral.med.uottawa.ca/",
"entryurl": "http://www.oxfordjournals.org/nar/database/summary/383",
"desc": "The Subviral RNA database contains a large number of sequences and related data on viroids, viroid-like RNAs and human hepatitis delta virus (vHDV) in a customizable and user-friendly format. In addition to the sequences themselves, many entries include additional data (e.g. position and secondary structures of the self-catalytic RNAs, prediction of the most stable secondary structures, multiple sequence aligments, duplicated sequences, etc.). Moreover, links are provided to the original GenBank, EMBL and Medline records. This database is available on the World Wide Web at http://penelope.med.usherb.ca/subviral/.",
"ref": null,
"absurl": "http://nar.oxfordjournals.org/cgi/content/abstract/31/1/444",
"email": "map@penelope.med.usherb.ca"
},
{
"name": "TarBase",
"url": "http://microrna.gr/tarbase",