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ViroBLAST read me
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Introduction to the standalone ViroBLAST server | |
Introduction | |
This standalone ViroBLAST server suite of programs was | |
designed to be similar to the NCBI BLAST server and | |
command-line NCBI C++ Toolkit BLAST applications referred as | |
the BLAST+ applications. It incorporates most | |
features that exist in NCBI BLAST+ program, and adds new | |
features to extend the utility of BLAST. It was created to | |
facilitate verification of the origins of Human | |
Immunodeficiency Virus (HIV) sequences derived from various | |
experiments, and then was developed into the standalone web | |
server for maximum utility in other research fields. It is | |
recommended that users have experience in installation and | |
running standalone NCBI BLAST+ programs when installing, | |
configuring and customizing ViroBLAST. After files are | |
uncompressed, ViroBLAST server is ready to be used | |
immediately. Users then can configure and customize sequence | |
databases to manage their own BLAST web server tailored to | |
meet their specific research purpose. | |
Features | |
* Customize public and user's local sequence databases. | |
* Blast against user's sequence data set by uploading | |
sequence file in FASTA format. | |
* Blast against multiple sequence databases selected by | |
user. | |
* Summarize the BLAST output and easily navigate the result. | |
* Download sequences in database that match user's query | |
sequence. | |
Installation of the standalone ViroBLAST server | |
After downloading the file viroblast.tar.gz, place it into | |
document directory of HTTPD server in your computer and | |
uncompress it by | |
gzip -d viroblast.tar.gz | |
tar -xvpf viroblast.tar | |
It is important to have the parameter "p" in tar options. It | |
will preserve file access options stored in the | |
distribution. Directory for the BLAST output (data) should | |
have readable, writeable and executable permissions for | |
everyone (777). | |
After you have uncompressed the distribution file, the | |
directory "viroblast" will be created. You can access the | |
ViroBLAST home page via URL: | |
http://your_hostname/viroblast/viroblast.php | |
Configuration of BLAST program | |
The standalone ViroBLAST server runs the NCBI BLAST+ | |
program and has been tested on Linux, Mac OS X and Sun OS. | |
The distribution comes with a standalone BLAST+ program for | |
linux ia32. It is your responsibility to download | |
appropriate standalone BLAST+ for your computer's operating | |
system from NCBI ftp site | |
(ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/). After you have | |
downloaded the standalone BLAST+, uncompress it and put in a | |
directory you want, then, change the path to "blast+" program | |
into server configuration file (viroblast.ini). | |
Configuration and customization of BLAST sequence databases | |
This distribution comes with 2 BLAST databases to test. | |
"Nucleotide test database" - sample nucleotide database and | |
"Protein test database" - sample protein database. These | |
databases are configured to be searchable immediately. After | |
testing, you need to set up your sequence databases for the | |
standalone ViroBLAST server. It is necessary to follow these | |
steps: | |
1. Put sequence FASTA file in appropriate directory under ./db/ | |
(./db/nucleotide/ or ./db/protein/). | |
2. Run "makeblastdb" program, available from the NCBI ftp site | |
(ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) | |
to format the sequence database. | |
3. Add name of the database into server configuration file | |
(viroblast.ini). | |
The format is: "database_file_name => database_name_for_display". | |
If there are more than one database, put comma "," between them. | |
Directories and Files in the distribution | |
* Root directory (./viroblast/): | |
- viroblast.php: viroblast home page. | |
- blastresult.php: blast result output page. | |
- blast.pl: perl program executes blast+ program and formats | |
the output. | |
- sequence.php: page showing sequences ready for download. | |
- download.php: download sequences | |
- viroblast.ini: Default configuration file for the ViroBLAST | |
server. | |
* ./viroblast/blast+/ | |
- Default standalone BLAST+ program for linux ia32 downloaded | |
from NCBI. | |
* ./viroblast/data/ | |
- Storage for BLAST output files. | |
* ./viroblast/docs/ | |
- Documents for the ViroBLAST server. | |
* ./viroblast/db/nucleotide/ | |
- Storage of nucleotide sequence databases for BLAST search. | |
* ./viroblast/db/protein/ | |
- Storage of protein sequence databases for BLAST search. | |
* ./viroblast/image/ | |
- Images used in ViroBLAST pages. | |
Server configuration file | |
This distribution comes with a default configuration file | |
"viroblast.ini". The configuration file will set the path to | |
blast+ program and what databases may be used with what | |
programs. | |
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