| Table 6.5. Databases available on BLAST Web server |
| Database/Description |
|
|
| A. Peptide Sequence Databases |
 |
nr |
|
All non-redundant GenBank CDS translations+RefSeq Proteins+PDB+SwissProt+PIR+PRF |
|
swissprot |
|
Last major release of the SwissProt protein sequence database (no updates) |
|
pat |
|
Proteins from the Patent division of GenPept |
|
Yeast |
|
Yeast (Saccharomyces cerevisiae) genomic CDS translations |
|
ecoli |
|
Escherichia coli genomic CDS translations |
|
pdb |
|
Sequences derived from the three-dimensional structure from Brookhaven Protein Data Bank |
|
Drosophila genome |
|
Drosophila genome proteins provided by Celera and Berkeley Drosophila Genome Project (BDGP) |
|
month |
|
All new or revised GenBank CDS translation+PDB+SwissProt+PIR+PRF released in the last 30 days |
| B. Nucleotide Sequence Databases |
|
nr |
|
All GenBank+RefSeq Nucleotides+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or phase 0, 1, or 2 HTGS sequences); no longer "non-redundant" |
|
est |
|
Database of GenBank+EMBL+DDBJ sequences from EST Divisions |
|
est_human |
|
Human subset of GenBank+EMBL+DDBJ sequences from EST Divisions |
|
est_mouse |
|
Mouse subset of GenBank+EMBL+DDBJ sequences from EST Divisions |
|
est_others |
|
Non-Mouse, non-Human sequences of GenBank+EMBL+DDBJ sequences from EST Divisions |
|
gss |
|
Genome survey sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences |
|
htgs |
|
Unfinished high-throughput genomic sequences: phase 0, 1, and 2 (finished, phase 3 HTG sequences are in nr) |
|
pat |
|
Nucleotides from the Patent division of GenBank |
|
|
yeast |
|
Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences |
|
|
mito |
|
Database of mitochondrial sequences |
|
|
vector |
|
Vector subset of GenBank(R), NCBI, in ftp://ftp.ncbi.nih.gov/blast/db |
|
|
E. coli |
|
Escherichia coli genomic nucleotide sequences |
|
|
pdb |
|
Sequences derived from the three-dimensional structure from Brookhaven Protein Data Bank |
|
|
Drosophila genome |
|
Drosophila genome provided by Celera and Berkeley Drosophila Genome Project (BDGP) |
|
|
month |
|
All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last 30 days |
|
|
alu |
|
Select Alu repeats from REPBASE, suitable fro masking Alu repeats from query sequences. It is available by anonymous FTP from ftp.ncbi.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski (1994) |
|
|
dbsts |
|
Database of GenBank+EMBL+DDBJ sequences from STS Divisions |
|
|
chromosome |
|
Searches complete genomes, complete chromosome, or contigs from the NCBI Reference Sequence project |
|
| C. Human Genome Blast Databases |
|
genome |
|
Human genomic contig sequences with NT_#### accessions |
|
|
mrna |
|
Human RefSeq mrna with NM_#### or XM_#### accessions |
|
|
protein |
|
Human RefSeq proteins with NP_#### or XP_#### accessions |
|
|
gscan mrna |
|
Predicted mRNA sequences generated by running GenomeScan program on human genomic contigs |
|
|
gscan protein |
|
CDS translations from gscan mrna set |
|
| D. CDD Search |
| Compares protein sequences to the conserved Domain Database. The CDD is a database containing a collection of functional and/or structural domain derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI. For more information, see the CDD homepage. |
|
|
| Source: http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#protein_databases
|
