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

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

yeast

Yeast (Saccharomyces cerevisiae) protein sequences.

E. coli

E. coli genomic CDS translations

pdb

Sequences derived from the 3-dimensional structure 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 Non-redundant GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences)

month

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

dbest

Non-redundant Database of GenBank+EMBL+DDBJ EST Divisions

dbsts

Non-redundant Database of GenBank+EMBL+DDBJ STS Divisions

htgs

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

yeast

Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences

E. coli

E. coli genomic nucleotide sequences

pdb

Sequences derived from the 3-dimensional structure

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

gss

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