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.