Skip to content

Instantly share code, notes, and snippets.

@mfcovington

mfcovington/reference-sequences-formatted.md

Created August 18, 2015 20:35
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save mfcovington/26929124fdd8c2ad48d6 to your computer and use it in GitHub Desktop.
Save mfcovington/26929124fdd8c2ad48d6 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
reference-sequences-formatted.md

CDS and Peptide Reference Sequences

Solanum lycopersicum:

  • Ensemble

    • CDS: ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.4_release/ITAG2.4_cds.fasta
    • PEP: ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.4_release/ITAG2.4_proteins_full_desc.fasta

  • SolGenomics

    • CDS: ftp://ftp.ensemblgenomes.org/pub//release-28/plants/fasta/solanum_lycopersicum/cds/Solanum_lycopersicum.GCA_000188115.2.28.cds.all.fa.gz
    • PEP: ftp://ftp.ensemblgenomes.org/pub//release-28/plants/fasta/solanum_lycopersicum/pep/Solanum_lycopersicum.GCA_000188115.2.28.pep.all.fa.gz

Solanum pennellii:

  • SolGenomics
    • CDS: ftp://ftp.solgenomics.net/genomes/Solanum_pennellii/annotations/Spenn-v2-cds-annot.fa
    • PEP: ftp://ftp.solgenomics.net/genomes/Solanum_pennellii/annotations/Spenn-v2-aa-annot.fa

Oryza sativa:

  • Ensemble

    • CDS: cds/oryza-sativa ftp://ftp.ensemblgenomes.org/pub/release-28/plants/fasta/oryza_sativa/cds/Oryza_sativa.IRGSP-1.0.28.cds.all.fa.gz
    • PEP: pep/oryza-sativa ftp://ftp.ensemblgenomes.org/pub/release-28/plants/fasta/oryza_sativa/pep/Oryza_sativa.IRGSP-1.0.28.pep.all.fa.gz

  • http://rice.plantbiology.msu.edu/downloads_gad.shtml

    • CDS: ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.cds
    • PEP: ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.pep

Medicago truncatula:

  • Ensemble

    • CDS: ftp://ftp.ensemblgenomes.org/pub/release-28/plants/fasta/medicago_truncatula/cds/Medicago_truncatula.GCA_000219495.2.28.cds.all.fa.gz
    • PEP: ftp://ftp.ensemblgenomes.org/pub/release-28/plants/fasta/medicago_truncatula/pep/Medicago_truncatula.GCA_000219495.2.28.pep.all.fa.gz

  • http://jcvi.org/medicago/display.php?pageName=General&section=Download

    • CDS: ftp://ftp.jcvi.org/pub/data/m_truncatula/Mt4.0/Annotation/Mt4.0v1/Mt4.0v1_GenesCDSSeq_20130731_1800.fasta
    • PEP: ftp://ftp.jcvi.org/pub/data/m_truncatula/Mt4.0/Annotation/Mt4.0v1/Mt4.0v1_GenesProteinSeq_20130731_1800.fasta

Arabidopsis thaliana:

  • Ensemble

    • CDS: ftp://ftp.ensemblgenomes.org/pub/release-28/plants/fasta/arabidopsis_thaliana/cds/Arabidopsis_thaliana.TAIR10.28.cds.all.fa.gz
    • PEP: ftp://ftp.ensemblgenomes.org/pub/release-28/plants/fasta/arabidopsis_thaliana/pep/Arabidopsis_thaliana.TAIR10.28.pep.all.fa.gz

  • https://www.arabidopsis.org/download_files/Sequences/TAIR10_blastsets/

    • CDS: https://www.arabidopsis.org/download_files/Sequences/TAIR10_blastsets/TAIR10_cds_20110103_representative_gene_model_updated
    • PEP: https://www.arabidopsis.org/download_files/Sequences/TAIR10_blastsets/TAIR10_pep_20110103_representative_gene_model_updated
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment