Supercomputer

Using the Databases

We acquire and set the latest versions of major biological databases such as GenBank, EMBL, and RefSeq, providing high-speed access without the need to transfer data over the Internet. Each database is set in a format that enables BLAST searches (e.g., Flat format, FASTA format). This resource is available for all research purposes.

Last Updated: December 25, 2008.

Announcements

Notes on various databases that can be used in Sun Blade 6048 Modular.

  • GenBank-UPD, EMBL-UPD and RefSeq-UPD are updated daily.
  • PDB, UniProt and PROSITE are updated every Thursday.
  • Databases other than those above are updated at the time of each new release.
    Please check for updates using the 'dbinfo' command. % dbinfo
  • By specifying an alias file as a target database in a BLAST search, it is possible to search multiple BLAST files:
    % blastall -d /usr/local/db/blast/genbank-upd/genbank -p blastn -i ~/query It is possible to search all GenBank release files and all updated files by executing the above command.
    (Note that the extension of the alias file must be removed.)

    To confirm the path of the alias file and the target database, please refer to the information below.
    Target databasePath of the alias file
    All release files of GenBank/usr/local/db/blast/genbank/genbank-rel.nal
    Release + update of GenBank/usr/local/db/blast/genbank-upd/genbank.nal
    Release + update of GenPept/usr/local/db/blast/genpept-upd/genpept.pal
    All release files of EMBL/usr/local/db/blast/embl/embl-rel.nal
    Release + update of EMBL/usr/local/db/blast/embl-upd/embl.nal
    RefSeq-Genomic + RefSeq-RNA/usr/local/db/blast/refseq/refseq-na-rel.nal
    Release + update of RefSeq
    Genomic + RNA
    /usr/local/db/blast/refseq-upd/refseq.nal
    Release + update of RefSeq
    Protein
    /usr/local/db/blast/refseq-upd/refseq.pal
    Swissprot + TrEMBL/usr/local/db/blast/uniprot/uniprot.pal
    NCBI nt + EST + GSS + HTGS + STS + patnt + WGS/usr/local/db/blast/ncbi/ncbi.nal
  • Refer to the chart below for the location path of each database file and additional details.
    (Example) The location path of a blast format file of GenBank | under /bio/db/blast/genbank/
    Database namePath(/bio/db/)Detail of the located file
    (compressed file located after extracting)
    GenBankflat/genbank/*.seq files at ftp://ftp.ncbi.nih.gov/genbank/
    fasta/Above files converted to FASTA format
    blast/Converted the above FASTA file to make it a target of a BLAST search
    GenBank-UPDflat/genbank-upd/All files at ftp://ftp.ncbi.nih.gov/genbank/daily-nc/
    fasta/*.flat files from above is converted to FASTA format
    blast/Converted the above FASTA file to make it a target of a BLAST search
    GenPept-genpept/-
    fasta/Translated the entry within the seq files of GenBank and converted to FASTA format
    blast/Converted the above FASTA file to make it a target of a BLAST search
    GenPept-UPD-genpept-upd/-
    fasta/Translated the entry within the *.flat files of GenBank-UPD and converted to FASTA format
    blast/Converted the above FASTA file to make it a target of a BLAST search
    EMBLflat/embl/*.dat files at ftp://ftp.ebi.ac.uk/pub/databases/embl/release/
    fasta/Above files converted to FASTA format
    blast/Converted the above FASTA file to make it a target of a BLAST search
    EMBL-UPDflat/embl-upd/All files at ftp://ftp.ebi.ac.uk/pub/databases/embl/new/
    fasta/r*.dat files from above is converted to FASTA format
    blast/Converted the above FASTA file to make it a target of a BLAST search
    RefSeq-Genomicflat/refseq/All files at ftp://ftp.ncbi.nih.gov/refseq/release/
    fasta/Files each combined *.genomic.fna included in each directory under /bio/db/flat/refseq/
    blast/Converted the above FASTA file to make it a target of a BLAST search
    RefSeq-RNAflat/refseq/Same as RefSeq-Genomic
    fasta/Files each combined *.rna.fna included in each directory under /bio/db/flat/refseq/
    blast/Converted the above FASTA file to make it a target of a BLAST search
    RefSeq-Proteinflat/refseq/Same as RefSeq-Genomic
    fasta/Files each combined *.protein.faa included in each directory under /bio/db/flat/refseq/
    blast/Converted the above FASTA file to make it a target of a BLAST search
    RefSeq-UPD-NAflat/refseq-upd/All files at ftp://ftp.ncbi.nih.gov/refseq/daily/
    fasta/Files combined rsnc.*.*.fna under /daily
    blast/Converted the above FASTA file to make it a target of a BLAST search
    RefSeq-UPD-AAflat/refseq-upd/Same as RefSeq-UPD-NA
    fasta/Files combined rsnc.*.*.fna under /daily
    blast/Converted the above FASTA file to make it a target of a BLAST search
    UniProtflat/uniprot/All files at ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/
    fasta/Target file of Swiss-Prot, TrEMBL
    blast/Target file of Swiss-Prot, TrEMBL
    Swiss-Prot
    (install as part of UniProt)
    flat/uniprot/Same as UniProt
    fasta/Copied uniprot_trembl.fasta and uniprot_trembl_varsplic from flat/
    blast/Converted the above FASTA file to make it a target of a BLAST search
    TrEMBL
    (install as part of UniProt)
    flat/uniprot/Same as UniProt
    fasta/Copied uniprot_trembl.fasta and uniprot_trembl_varsplic from flat/
    blast/Converted the above FASTA file to make it a target of a BLAST search
    NCBI-nt-ncbi/-
    fasta/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz
    blast/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/nt.*.tar.gz
    NCBI-nr-ncbi/-
    fasta/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
    blast/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/nr.*.tar.gz
    NCBI-dbEST-ncbi/-
    fasta/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/est_*.gz
    blast/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/est.*.tar.gz
    NCBI-dbGSS-ncbi/-
    fasta/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/gss.gz
    blast/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/gss.*.tar.gz
    NCBI-HTGS-ncbi/-
    fasta/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/htgs.gz
    blast/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/htgs.*.tar.gz
    NCBI-STS-ncbi/-
    fasta/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/sts.gz
    blast/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/sts.tar.gz
    NCBI-patnt-ncbi/-
    fasta/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/patnt.gz
    blast/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/patnt.tar.gz
    NCBI-WGS-ncbi/-
    fasta/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/FASTA/wgs.gz
    blast/Located after extracting ftp://ftp.ncbi.nih.gov/blast/db/wgs.*.tar.gz
    PDBflat/pdb/All files at ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/pdb/
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    EPDflat/epd/All files at ftp://ftp.epd.isb-sib.ch/epd/current/
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    PROSITEflat/prosite/All files at ftp://au.expasy.org/databases/prosite/release_with_updates/
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    --
    Pfamflat/pfam/All files at ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/
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