blast/docs/blast_databases.html
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<TITLE>Databases available for BLAST search</TITLE>
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<h1 align="center">Databases available for BLAST search</h1>
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<h3> Peptide Sequence Databases</h3>
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<dl>
<dt><b>nr</b>
<dd>All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF
<p>
<dt><b>month</b>
<dd>All new or revised GenBank CDS translation+PDB+SwissProt+PIR+PRF released in
the last 30 days.
<p>
<dt><b>swissprot</b>
<dd>the last major release of the SWISS-PROT protein sequence
database (no updates)
<p>
<dt><b>yeast</b>
<dd>Yeast (Saccharomyces cerevisiae) protein sequences.
<p>
<dt><b>E. coli</b>
<dd>E. coli genomic CDS translations
<p>
<dt>
<b>pdb</b>
<dd>Sequences derived from the 3-dimensional structure
Brookhaven Protein Data Bank
<p>
<dt><b>kabat</b> [kabatpro]
<dd>Kabat's database of sequences of immunological interest
<p>
<dt><b>alu</b>
<dd>Translations of select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994) .
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<dt>
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<h3>Nucleotide Sequence Databases</h3>
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<p>
<dt><b>nr</b>
<dd>All Non-redundant GenBank+EMBL+DDBJ+PDB sequences (but
no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences)
<p>
<dt>
<b>month</b>
<dd>All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last
30 days.
<p>
<dt>
<b>dbest</b>
<dd> Non-redundant Database of GenBank+EMBL+DDBJ EST Divisions
<p>
<dt><b>dbsts</b>
<dd>Non-redundant Database of GenBank+EMBL+DDBJ STS Divisions
<p>
<dt>
<b>htgs</b>
<dd> htgs unfinished High Throughput Genomic Sequences: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr)
<p>
<dt><b>yeast</b>
<dd>Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences
<p>
<dt><b>E. coli</b>
<dd>E. coli genomic nucleotide sequences
<p>
<dt><b>pdb</b>
<dd>Sequences derived from the 3-dimensional structure
<p>
<dt><b>kabat</b> [kabatnuc]
<dd>Kabat's database of sequences of immunological interest
<p>
<dt><b>vector</b>
<dd>Vector subset of GenBank(R), NCBI, in ftp://ncbi.nlm.nih.gov/blast/db/
<p>
<dt><b>mito</b>
<dd>Database of mitochondrial sequences"
<p>
<dt><b>alu</b>
<dd>Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994).
<p>
<dt><b>epd</b>
<dd>Eukaryotic Promotor Database
<p>
<dt><b>gss</b>
<dd>Genome Survey Sequence, includes single-pass genomic data, exon-trapped
sequences, and Alu PCR sequences.
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