# 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) .

### Nucleotide Sequence Databases

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.