Databases available for BLAST search

Peptide Sequence Databases

nr

All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF

month

All new or revised GenBank CDS translation+PDB+SwissProt+PIR+PRF released in the last 30 days.

swissprot

Last major release of the SWISS-PROT protein sequence database (no updates)

Drosophila genome

Drosophila genome proteins provided by Celera and Berkeley Drosophila Genome Project (BDGP).

yeast

Yeast (Saccharomyces cerevisiae) genomic CDS translations

ecoli

Escherichia coli genomic CDS translations

pdb

Sequences derived from the 3-dimensional structure from Brookhaven Protein Data Bank

kabat [kabatpro]

Kabat's database of sequences of immunological interest

alu

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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Nucleotide Sequence Databases

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nr

All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences). No longer "non-redundant".

month

All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last 30 days.

Drosophila genome

Drosophila genome provided by Celera and Berkeley Drosophila Genome Project (BDGP).

dbest

Database of GenBank+EMBL+DDBJ sequences from EST Divisions

dbsts

Database of GenBank+EMBL+DDBJ sequences from STS Divisions

htgs

Unfinished High Throughput Genomic Sequences: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr)

gss

Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.

yeast

Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences

E. coli

Escherichia coli genomic nucleotide sequences

pdb

Sequences derived from the 3-dimensional structure from Brookhaven Protein Data Bank

kabat [kabatnuc]

Kabat's database of sequences of immunological interest

vector

Vector subset of GenBank(R), NCBI, in ftp://ncbi.nlm.nih.gov/blast/db/

mito

Database of mitochondrial sequences

alu

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).

epd

Eukaryotic Promotor Database found on the web at http://www.genome.ad.jp/dbget-bin/www_bfind?epd

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Trace Archive Databases

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The sequences in these databases are derived from raw sequence trace files. These data are not trimmed for quality or vector sequences. The trace files in the Trace Archive are from a variety of projects and strategies, including Whole Genome Shotgun (WGS), Clone by Clone Strategies, BAC end sequencing, and EST sequencing.

organism-WGS

Whole Genome Shotgun reads

organism-EST

EST reads

organism-other

Any other trace file - mostly BAC traces and BAC end sequences

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