databases
Databases
Resources from National Library of Medicine (NLM)
- GenBank annotated collection of all publicly available DNA sequences
- a genetic sequence data repository
- provides tools for searching and manipulating its contents, which have been a boon to molecular biologists and have helped advance developments in the field. From here
- Molecular Modeling Database (MMDB)
- OMIM (Online Mendelian Inheritance in Man)- 15,000 entries detailing clinical phenotypes and disorders as well as information on nearly 9,000 genes
- LocusLink
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites. Sequence accessions include a subset of GenBank accessions for a locus, as well as a new type, the NCBI Reference Sequence (RefSeq). serves as a switchboard to integrate these resources together as well as provide annotation of the gene's function using the widely accepted GeneOntology
UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProt is comprised of three components, each optimized for different uses. The UniProt Knowledgebase (UniProt) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Non-redundant Reference (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences.
Others Databases
- Transfact Database
- EMBL-EBI: European Bioinformatics Institute biological databases
- Swiss-Prot : the UniProt/Swiss-Prot Protein Knowledgebase is an annotated protein sequence database .
- TAMBIS aims to aid researchers in biological science by providing a single access point for biological information sources round the world.
- InterPro : InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
- Brenda - The Comprehensive Enzyme Information System
- Kinase : collection of protein kinase sequences grouped into families by homology of their catalytic domains.
- MeSH (Medical Subject Heading: controlled vocabularies of biomedical terms)
- KEGG : Kyoto Encyclopedia of Genes and Genomes
- Dip : database of interacting proteins
- Pir : catalog of macromolecular complexes
- Bind : (Biomolecular Interaction Network Database) curate and archive physical interactions between biomolecules from the literature using a standard data representation so that they may be effectively used for knowledge discovery
- MINT: Molecular Interactions database
- GeNet: database of regulatory gen networks
- TRANSPATH: database of regulatory gen networks
- CSNDB: database of signaling pathways
- SPAD: database of signaling pathways
- MINT
- BindDB: knowledge base of diverse molecular interactions and associated affinity information
- COMPEL: compendium of protein-DNA interactions
- YPD (Yeast Protein Database), now defunct
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae.
- BIND Biomolecular Interaction Network Database
- GenomeWeb a list of protein interaction databases
Model organism genome databases
- FlyBase publically available database on the genetics and molecular biology of Drosophila (fruitflies).
- Wormbase
- EcoCyc (Electronic encyclopedia of E. coli genes and metabolism)