List of biological databases
- 1 Primary nucleotide sequence databases
- 2 Meta Databases
- 3 Genome databases
- 4 Protein sequence databases
- 5 Proteomics databases
- 6 Protein structure databases
- 7 Protein model databases
- 8 RNA databases
- 9 Carbohydrate structure databases
- 10 Protein-protein interactions
- 11 Signal transduction pathway databases
- 12 Metabolic pathway databases
- 13 Microarray databases
- 14 Exosomal databases
- 15 Mathematical model databases
- 16 PCR and quantitative PCR primer databases
- 17 Specialized databases
- 18 Taxonomic databases
- 19 Wiki-style databases
- 20 References
Primary nucleotide sequence databases
The International Nucleotide Sequence Database (INSD) consists of the following databases.
- DNA Data Bank of Japan (National Institute of Genetics)
- European Nucleotide Archive (European Bioinformatics Institute)
- GenBank (National Center for Biotechnology Information)
The three databases, DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe), are repositories for nucleotide sequence data from all organisms. All three databases accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them. These three databases are primary databases, as they house original sequence data.
These databases of databases collect data from different sources and make them available in new and more convenient form, or with an emphasis on a particular disease or organism.
- BioGraph (University of Antwerp, Vlaams Instituut voor Biotechnologie) A knowledge discovery service based on the integration of more than 20 heterogeneous databases
- Bioinformatic Harvester (Karlsruhe Institute of Technology) - Integrating 26 major protein/gene resources.
- Neuroscience Information Framework (University of California San Diego) - Integrates hundreds of neuroscience relevant resources, many are listed below.
- ConsensusPathDB - A molecular functional interaction database, integrating information from 12 other databases.
- Entrez (National Center for Biotechnology Information)
- Enzyme Portal Integrates enzyme information such as small-molecule chemistry, biochemical pathways and drug compounds. (European Bioinformatics Institute)
- euGenes (Indiana University)
- GeneCards (Weizmann Inst.)
- MetaBase (KOBIC) - A user contributed database of biological databases.
- mGen containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
- PathogenPortal A repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID)
- SOURCE (Stanford University) encapsulates the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, and Rattus norvegicus into easy to navigate GeneReports
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.
- Bioinformatic Harvester
- CAMERA Resource for microbial genomics and metagenomics
- Corn, the Maize Genetics and Genomics Database
- EcoCyc a database that describes the genome and the biochemical machinery of the model organism E. coli K-12
- Ensembl provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes.
- Ensembl Genomes provides genome-scale data for bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces (using the Ensembl software platform).
- PATRIC, the PathoSystems Resource Integration Center
- Flybase, genome of the model organism Drosophila melanogaster
- MGI Mouse Genome (Jackson Lab.)
- JGI Genomes of the DOE-Joint Genome Institute provides databases of many eukaryote and microbial genomes.
- National Microbial Pathogen Data Resource. A manually curated database of annotated genome data for the pathogens Campylobacter, Chlamydia, Chlamydophila, Haemophilus, Listeria, Mycoplasma, Neisseria, Staphylococcus, Streptococcus, Treponema, Ureaplasma, and Vibrio.
- RegulonDB RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell E. coli K-12.
- Saccharomyces Genome Database, genome of the yeast model organism.
- Viral Bioinformatics Resource Center Curated database containing annotated genome data for eleven virus families.
- The SEED platform for microbial genome analysis includes all complete microbial genomes, and most partial genomes. The platform is used to annotate microbial genomes using subsystems.
- Xenbase, genome of the model organism Xenopus tropicalis and Xenopus laevis
- Wormbase, genome of the model organism Caenorhabditis elegans
- Zebrafish Information Network, genome of this fish model organism.
- TAIR, The Arabidopsis Information Resource.
- UCSC Malaria Genome Browser, genome of malaria causing species (Plasmodium falciparumata and others)
- RGD Rat Genome Database: Genomic and phenotype data for Rattus norvegicus
-  INTEGRALL: Database dedicated to integrons, bacterial genetic elements involved in the antibiotic resistance
- Fourmidable ant genome database provides ant genome blast search and sequence download.
- VectorBase The NIAID Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens
- EzGenome, comprehensive information about manually curated genome projects of prokaryotes (archaea and bacteria) 
Protein sequence databases
- UniProt Universal Protein Resource (EBI, Swiss Institute of Bioinformatics, PIR)
- Protein Information Resource (Georgetown University Medical Center (GUMC))
- Swiss-Prot Protein Knowledgebase (Swiss Institute of Bioinformatics)
- PEDANT Protein Extraction, Description and ANalysis Tool (Forschungszentrum f. Umwelt & Gesundheit)
- PROSITE Database of Protein Families and Domains
- Database of Interacting Proteins (Univ. of California)
- Pfam Protein families database of alignments and HMMs (Sanger Institute)
- PRINTS a compendium of protein fingerprints from (Manchester University)
- ProDom Comprehensive set of Protein Domain Families (INRA/CNRS)
- SignalP 3.0 Server for signal peptide prediction (including cleavage site prediction), based on artificial neural networks and HMMs
- SUPERFAMILY Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms
- Annotation Clearing House a project from the National Microbial Pathogen Data Resource
- InterPro Classifies proteins into families and predicts the presence of domains and sites.
- Proteomics Identifications Database (PRIDE) A public repository for proteomics data, containing protein and peptide identifications and their associated supporting evidence as well as details of post-translational modifications. (European Bioinformatics Institute)
- MitoMiner - A mitochondrial proteomics database integrating large-scale experimental datasets from mass spectrometry and GFP studies for 12 species. (MRC Mitochondrial Biology Unit)
Protein structure databases
Protein Data Bank (PDB) comprising:
- Protein DataBank in Europe (PDBe)
- ProteinDatabank in Japan (PDBj)
- Research Collaboratory for Structural Bioinformatics (RCSB)
For more protein structure databases, see also Protein structure database
Protein model databases
- Swiss-model Server and Repository for Protein Structure Models
- ModBase Database of Comparative Protein Structure Models (Sali Lab, UCSF)
- Protein Model Portal (PMP) Meta database that combines several databases of protein structure models (Biozentrum, Basel, Switzerland)
- Rfam , a database of RNA families
- miRBase , the microRNA database
- snoRNAdb, a database of snoRNAs
- lncRNAdb, a database of lncRNAs
- piRNAbank, a database of piRNAs
- GtRNAdb, a database of genomic tRNAs
- SILVA, a database of ribosomal RNAs
- RDP, the Ribosomal Database Project
- tmRDB, a database of tmRNAs
- SRPDB, a database of signal recognition particle RNAs
- yeast snoRNA database
- Sno/scaRNAbase, a database of snoRNA and scaRNAs
- snoRNA-LBME-db, a snoRNA database
Carbohydrate structure databases
- BIND Biomolecular Interaction Network Database
- BioGRID  A General Repository for Interaction Datasets (Samuel Lunenfeld Research Institute)
- CCSB Interactome
- DIP Database of Interacting Proteins
- IntAct molecular interaction database: a central, standards-compliant repository of molecular interactions, including protein–protein, protein–small molecule and protein–nucleic acid interactions.
- STRING: STRING is a database of known and predicted protein-protein interactions. (EMBL)
- The Cell Collective
- MINT: Molecular INTeraction database
Signal transduction pathway databases
- Cancer Cell Map
- Netpath - A curated resource of signal transduction pathways in humans
- NCI-Nature Pathway Interaction Database
- Reactome - Navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling.
- SignaLink Database
- The Cell Collective
Metabolic pathway databases
- Small Molecule Pathway Database (SMPDB)
- BioCyc Database Collection including EcoCyc and MetaCyc
- KEGG PATHWAY Database (Univ. of Kyoto)
- MANET database  (University of Illinois)
- Metabolights Metabolomics experiments and derived information: metabolite structures, reference spectra, biological roles, locations and concentrations. (European Bioinformatics Institute)
- Reactome Navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling. (Cold Spring Harbor Laboratory, European Bioinformatics Institute, Gene Ontology Consortium)
- ArrayExpress (European Bioinformatics Institute)
- Gene Expression Omnibus (National Center for Biotechnology Information)
- GPX(Scottish Centre for Genomic Technology and Informatics)
- maxd (Univ. of Manchester)
- Stanford Microarray Database (SMD) (Stanford University)
- Genevestigator - Expression Search Engine (Nebion AG)
Mathematical model databases
- Biomodels Database: published mathematical models describing biological processes.
- The Cell Collective: build and simulate large-scale models in real-time and in a highly collaborative fashion
PCR and quantitative PCR primer databases
- PathoOligoDB: A free QPCR oligo database for pathogens
- RTPrimerDB - a public primers and probes database for real-time PCR reactions
- Antibody Central Antibody information database and search resource.
- AntibodyRegistry.org assigns unique identifiers used to track antibody reagents in published literature.
- BIOMOVIE (ETH Zurich) movies related to biology and biotechnology
- BioNumbers a database of useful biological numbers
- CGAP Cancer Genes (National Cancer Institute)
- Clone Registry Clone Collections (National Center for Biotechnology Information)
- Connectivity map Transcriptional expression data and correlation tools for drugs
- CTD The Comparative Toxicogenomics Database describes chemical-gene-disease interactions
- DBGET H.sapiens (Univ. of Kyoto)
- DiProDB A database to collect and analyse thermodynamic, structural and other dinucleotide properties.
- Drug2Gene Provides integrated information for identified and reported relations between genes/proteins and drugs/compounds
- Dryad a repository of data underlying scientific publications in the basic and applied biosciences.
- Edinburgh Mouse Atlas
- GreenPhylDB (A phylogenomic database for plant comparative genomics)
- GDB Hum. Genome Db (Human Genome Organisation)
- HGMD disease-causing mutations (HGMD Human Gene Mutation Database)
- HUGO (Official Human Genome Database: HUGO Gene Nomenclature Committee)
- HvrBase++ Human and primate mitochondrial DNA
- INTERFEROME The Database of Interferon Regulated Genes
- List with SNP-Databases
- Minimotif Miner -Database of short contiguous functional peptide motifs
- NCBI-UniGene (National Center for Biotechnology Information)
- Oncogenomic databases A compilation of databases that serve for cancer research.
- OMIM Inherited Diseases (Online Mendelian Inheritance in Man)
- OrthoMaM (A database of Orthologous Mammalian Markers)
- OrthoMCL Ortholog Groups of Protein Sequences from Multiple Genomes including Archaea, Bacteria and Eukaryotes.
- p53 The p53 Knowledgebase
- PhenCode linking human mutations with phenotype
- PhenomicDB multi-organism database linking genotype to phenotype
- PHI-base Pathogen-host interaction database. It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer reviewed literature.
- Plasma Proteome Database Human plasma proteins along with their isoforms
- SABIO-RK SABIO-RK is a curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions.
- SciClyc An Open-access database to shared antibodies, cell cultures, and documents for biomedical research.
- SHMPD The Singapore Human Mutation and Polymorphism Database
- SNPSTR database A database of SNPSTRs - compound genetic markers consisting of a microsatellite (STR) and one tightly linked SNP - in human, mouse, rat, dog and chicken.
- TDR Targets A chemogenomics database focused on drug discovery in tropical diseases.
- TRANSFAC A database about eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles.
- TreeBASE An open-access database of phylogenetic trees and the data behind them
- Treefam TreeFam (Tree families database) is a database of phylogenetic trees of animal genes
- XTractor Discovering Newer Scientific Relations Across PubMed Abstracts. A tool to obtain manually annotated relationships for Proteins, Diseases, Drugs and Biological Processes as they get published in PubMed.
- Catalogue of Life source databases
- Encyclopedia of Life
- Integrated Taxonomic Information System
- EzTaxon-e, database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
- Gene Wiki