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.