| A. Peptide sequence databases |
| nr |
All nonredundant 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
“nonredundant”
|
| 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: phases 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 for masking Alu repeats from query sequences. 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 domains derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI. For more
information, see the CDD homepage.
|
