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.


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Acknowledgements
   The Gene Index Project is supported in part by funding from the US National Science Foundation through grant #DBI-0552416.