Databases available for BLAST search
Peptide Sequence Databases
- alu (NCBI)
- 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) .
-
drosoph (NCBI)
- Drosophila genome proteins provided by Celera and Berkeley Drosophila
Genome Project (BDGP).
- ecoli (NCBI)
- Escherichia coli genomic CDS translations.
- igallaaseq (NCBI)
- Kabat database of sequences of
immunological interest.
- migallaaseq (NCBI)
- Kabat database of sequences of
immunological interest.
- month (NCBI)
- All new or revised GenBank CDS translations+PDB+SwissProt+PIR+PRF released
in the last 30 days.
- nr (NCBI)
- All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF.
- pataa (NCBI)
- Protein sequences derived from the Patent division of GenBank.
- pdbaa (NCBI)
- Sequences derived from the 3-dimensional from the Protein
Data Bank.
- swissprot (NCBI)
- SWISS-PROT protein sequence database.
- yeast (NCBI)
- Yeast (Saccharomyces cerevisiae) genomic CDS translations.
- ARG (TIGR)
- Methanococcus
jannaschii - complete genome.
- BTM (TIGR)
- Thermotoga
maritima - complete genome.
- GAF (TIGR)
- Archaeoglobus
fulgidus - complete genome.
- GBB (TIGR)
- Borrelia
burgdorferi - complete genome.
- GHI (TIGR)
- Haemophilus
influenzae - complete genome.
- GHP (TIGR)
- Heliobacter
pylori - complete genome.
- GMG (TIGR)
- Mycoplasma
genitalium - complete genome.
- GMT (TIGR)
- Mycobacterium
tuberculosis - complete genome.
- GTP (TIGR)
- Treponema
pallidum Nichols - complete genome.
-
Nucleotide Sequence Databases
-
- alu (NCBI)
- Select Alu repeats from REPBASE, suitable for masking Alu repeats from query
sequences.
- drosoph (NCBI)
- Drosophila genome provided by Celera and Berkeley Drosophila
Genome Project (BDGP).
-
- ecoli (NCBI)
- Escherichia coli genomic nucleotide sequences.
- est_human (NCBI)
- Non-redundant Database of Human GenBank+EMBL+DDBJ EST sequences from EST
Divisions.
- est_mouse (NCBI)
- Non-redundant Database of Mouse GenBank+EMBL+DDBJ EST sequences.
- est_others (NCBI)
- Non-redundant Database of all other organisms GenBank+EMBL_DDBJ EST sequences.
- gss (NCBI)
- Genome Survey Sequence,
includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.
- htg (NCBI)
- Unfinished High Throughput Genomic
Sequences: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr).
- igallncseq (NCBI)
- Kabat database of sequences of
immunological interest.
- migallncseq (NCBI)
- Kabat database of sequences of
immunological interest.
- modjgene (NCBI)
- Kabat database of sequences of
immunological interest.
- month (NCBI)
- All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last
30 days.
- nt (NCBI)
- All Non-redundant GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
or HTGS sequences).
- patnt (NCBI)
- Nucleotide sequences derived from the Patent divison of GenBank.
- pdbnt (NCBI)
- Sequences derived from the 3-dimensional from the Protein
Data Bank.
- sts (NCBI)
- Non-redundant Database of GenBank+EMBL+DDBJ STS Divisions.
- vector (NCBI)
- Vector subset of GenBank (R), NCBI, in ftp://ftp.ncbi.nlm.nih.gov/blast/db/.
- yeast (NCBI)
- Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences.
- ARG (TIGR)
- Methanococcus
jannaschii - complete genome.
- BTM (TIGR) and BTM.1 (TIGR)
- Thermotoga
maritima - complete genome.
- GAF (TIGR)
- Archaeoglobus
fulgidus - complete genome.
- GBB (TIGR)
- Borrelia
burgdorferi - complete genome.
- GHI (TIGR)
- Haemophilus
influenzae - complete genome.
- GHP (TIGR)
- Heliobacter
pylori - complete genome.
- GMG (TIGR)
- Mycoplasma
genitalium - complete genome.
- GMT (TIGR)
- Mycobacterium
tuberculosis - complete genome.
- GTP (TIGR) and GTP.1 (TIGR)
- Treponema
pallidum Nichols - complete genome.
- estfa1 (TIGR)
- Human - 346 ESTs
from Adams, et. al., Science (1991) 252:1651-1656.
- estfa2 (TIGR)
- Human - 2298 ESTs
from Adams, et. al., Nature (1992) 355:632-634.
- estfa3 (TIGR)
- Human - 3394 ESTs
from Adams, et. al., Nature Genetics (1993) 4:256-267.
- estfa4 (TIGR)
- Human - 1825 ESTs
from Adams, et al, Nature Genetics (1993) 4:373-380.
- estfa5 (TIGR)
- Human - 8735 ESTs
from Adams, et al, submitted for publication.
- s_gordonii (TIGR)
- Streptococcus gordonii
- incomplete genome.
- westfa1 (TIGR)
- C. elegans
- 714 ESTs from McCombie, et al, Nature Genetics (1992), 1:124-31.