From: BBP: Brucella genome annotation with literature mining and curation
Resources | Databases and analysis programs | Comments |
---|---|---|
Databases | ||
NCBI | PubMed | Biomedical publications |
 | MeSH | Medical Subject Headings |
 | RefSeq | Reference sequences |
 | Genome | Genome summary |
 | Gene | Gene information |
 | Protein | Protein information |
 | Nucleotide | Nucleotide information |
 | CDD | conserved domains |
 | COGs | clusters of orthologous groups |
 | Taxonomy | Brucella taxonomy information |
 | 3D structure DB | 3D structures (typically of related proteins) |
 | Feature tables | Protein coding genes, functional and structural RNAs, |
EBI & SIB | Swissprot | Annotated protein data |
 | TrEMBL | protein data |
 | InterPro | protein families, domains and functions |
 | 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 |
 | TIGRfam | TIGRfam assignments |
Others | PFam | protein domains and families |
 | 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 |
 | TextPresso | NLP text mining |
 | PubSearch | literature curation management |
Other | BioPerl | Programming tools |