Biological databases

The following is an incomplete list of important biological databases commonly used in bioinformatics.

Primary sequence databases

The International Nucleotide Sequence Database (INSD) consists of the following databases.

1. DDBJ: DNA Data Bank of Japan
2. EMBL Nucleotide DB (European Molecular Biology Laboratory)
3. GenBank [1] (National Center for Biotechnology Information)

These databanks represent the current knowledge about the sequences of all organisms. They interchange the stored information and are the source for many other databases.

Meta-databases

Strictly speaking a meta-database can be considered a database of databases, rather than any one integration project or technology. They collect data from different sources and usually makes them available in new and more convenient form, or with an emphasis on a particular disease or organism.

1. Entrez (National Center for Biotechnology Information)
2. euGenes (Indiana University)
3. GeneCards (Weizmann Inst.)
4. SOURCE (Stanford University)
5. mGen containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
6. Bioinformatic Harvester (Karlsruhe Institute of Technology) — Integrating 26 major protein/gene resources.
7. MetaBase (KOBIC) &mdasdh; a user contributed database of biological databases.

Genome databases

These databases collect organism genome sequences, annotate and analyze them, and provide public access. Some add curation of experimental literature to improve computed annotations. These databases may hold many species genomes, or a single model organism genome.

1. Ensembl — provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes.
2. JGI Genomes of the DOE-Joint Genome Institute — provides databases of many eukaryote and microbial genomes.
3. CAMERA Resource for microbial genomics and metagenomics
4. MGI Mouse Genome (Jackson Laboratory)
5. Corn, the Maize Genetics and Genomics Database
6. Saccharomyces Genome Database — genome of the yeast model organism.
7. Wormbase — genome of the model organism Caenorhabditis elegans
8. Zebrafish Information Network — genome of this fish model organism.
9. ENCODE — database of known functional elements in human genome.

Genome browsers

Genome Browsers enable researchers to visualize and browse entire genomes (most have many complete genomes) with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc. Annotated data is usually from multiple diverse sources.

1. Integrated Microbial Genomes (IMG) system by the DOE-Joint Genome Institute
2. UCSC Genome Bioinformatics Genome Browser and Tools (UCSC)
3. Ensembl — The Ensembl Genome Browser (Sanger Institute and EBI)
4. GBrowse — The GMOD GBrowse Project
5. Pathway Tools Genome Browser
6. X:Map &mdsah; a genome browser that shows Affymetrix Exon Microarray hit locations alongside the gene, transcript and exon data on a Google maps api

Protein sequence databases

1. UniProt: Universal Protein Resource (UniProt Consortium: EBI, Expasy, Protein Information Resource)
2. PIR Protein Information Resource (Georgetown University Medical Center)
3. Swiss-Prot: Protein Knowledgebase (Swiss Institute of Bioinformatics)
4. PEDANT: Protein Extraction, Description and ANalysis Tool] (Forschungszentrum f. Umwelt & Gesundheit)
5. PROSITE — database of protein families and structural domains
6. DIP: Database of Interacting Proteins (University of California)
7. Pfam: Protein families — database of alignments and HMMs (Sanger Institute)
8. ProDom — comprehensive set of Protein Domain Families (Institut National de la Recherche Agronomique/Centre national de la recherche scientifique)
9. SignalP 3.0 &mdsah; server for signal peptide prediction (including cleavage site prediction), based on artificial neural networks and HMMs
10. SUPERFAMILY — library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms

Protein structure databases

1. PDB: Protein Data Bank (RCSB: Research Collaboratory for Structural Bioinformatics)
2. CATH Protein Structure Classification
3. SCOP: Structural Classification of Proteins
4. SWISS-MODEL — server and repository for protein structure models
5. ModBase — database of comparative protein structure models (Sali Lab, UCSF)

Protein-protein interactions

1. BioGRID — a general repository for interaction datasets (Samuel Lunenfeld Research Institute)
2. STRING — a database of known and predicted protein-protein interactions (EMBL)
3. DIP: Database of Interacting Proteins

Metabolic pathway databases

1. BioCyc Database Collection (including EcoCyc and MetaCyc)
2. KEGG PATHWAY Database (Kyoto University)
3. MANET database (University of Illinois)
4. Reactome (Cold Spring Harbor Laboratory, European Bioinformatics Institute, Gene Ontology Consortium)

Microarray databases

1. ArrayExpress (European Bioinformatics Institute)
2. Gene Expression Omnibus (National Center for Biotechnology Information)
3. maxd (University of Manchester)
4. SMD (Stanford University)
5. GPX (Scottish Centre for Genomic Technology and Informatics)

Mathematical model databases

1. CellML
2. Biomodels Database

PCR / Real time PCR primer databases

1. PathoOligoDB: A free QPCR oligo database for pathogens

Specialized databases

1. BIOMOVIE (ETH-Zurich) — movies related to biology and biotechnology
2. CGAP Cancer Genes (National Cancer Institute)
3. Clone Registry Clone Collections (National Center for Biotechnology Information)
4. DBGET H.sapiens (Kyoto University)
5. GDB Hum. Genome Db (Human Genome Organisation)
6. SHMPD: The Singapore Human Mutation and Polymorphism Database
7. NCBI-UniGene (National Center for Biotechnology Information)
8. OMIM Inherited Diseases (Online Mendelian Inheritance in Man)
9. Off. Hum. Genome Db (HUGO Gene Nomenclature Committee)
10. HGMD disease-causing mutations (HGMD Human Gene Mutation Database)
11. PhenCode linking human mutations with phenotype
12. List with SNP-Databases
13. p53: The p53 Knowledgebase
14. Edinburgh Mouse Atlas
15. HvrBase++: Human and primate mitochondrial DNA
16. PolygenicPathways &mdsh; genes and risk factors implicated in Alzheimer's disease, Bipolar disorder or Schizophrenia
17. Connectivity map — transcriptional expression data and correlation tools for drugs
18. CTD: The Comparative Toxicogenomics Database — describes chemical-gene-disease interactions