Table 1 Public databases and software programs linked or used in BBP. Unique database identifiers (e.g., RefSeq ID) are usually stored for linking to public database web pages. Brucella literature abstracts and full text PDF files are also extracted from PubMed. Software programs are integrated into BBP in different ways.
From: BBP: Brucella genome annotation with literature mining and curation
Resources | Databases and analysis programs | Comments |
|---|---|---|
Databases | ||
NCBI | PubMed | Biomedical publications |
| Â | MeSH | Medical Subject Headings |
| Â | RefSeq | Reference sequences |
| Â | Genome | Genome summary |
| Â | Gene | Gene information |
| Â | Protein | Protein information |
| Â | Nucleotide | Nucleotide information |
| Â | CDD | conserved domains |
| Â | COGs | clusters of orthologous groups |
| Â | Taxonomy | Brucella taxonomy information |
| Â | 3D structure DB | 3D structures (typically of related proteins) |
| Â | Feature tables | Protein coding genes, functional and structural RNAs, |
EBI & SIB | Swissprot | Annotated protein data |
| Â | TrEMBL | protein data |
| Â | InterPro | protein families, domains and functions |
| Â | PROSITE | protein families and domains |
TIGR | CMR | codon usage, EC numbers, condensed genome display, role category graph, GO terms, gene attribute, Role category gene list, RNAs, terminators |
| Â | TIGRfam | TIGRfam assignments |
Others | PFam | protein domains and families |
| Â | ProDom | protein domain families |
Software programs integrated | ||
NCBI | BLAST | Blastn, blastp, blastx, tblastn, tblastx, PSI/PHI Blast, Mega Blast, Blast 2 sequences |
GMOD | GBrowse | genome browse and analysis |
| Â | TextPresso | NLP text mining |
| Â | PubSearch | literature curation management |
Other | BioPerl | Programming tools |