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Biological Databases & Genome Technology Directory

A directory of the major biological databases — nucleotide, protein, structure, genome, pathway and variation resources — with reading on genome technology, gene expression, gene mapping and metabolic pathways.

50 topics•8 categories•Updated October 2026

Nucleotide & Genome Databases

8 entries

Sequence repositories and genome browsers.

01NCBIUS National Center for Biotechnology Information, hosting GenBank, PubMed, RefSeq and more. 02GenBankNIH genetic sequence database of annotated public DNA sequences. 03European Nucleotide Archive (ENA)EMBL-EBI's open archive of nucleotide sequencing data. 04DDBJDNA Data Bank of Japan, part of the international nucleotide sequence collaboration. 05RefSeqCurated, non-redundant reference sequences for genomes, transcripts and proteins. 06EnsemblGenome browser and annotation for vertebrates and other species. 07UCSC Genome BrowserInteractive genome browser with annotation tracks. 08NCBI GEOPublic repository of gene expression and functional genomics data.

Protein & Structure Databases

5 entries

Protein sequences, families and 3D structures.

09UniProtComprehensive protein sequence and functional information. 10RCSB Protein Data BankArchive of 3D structures of proteins and nucleic acids. 11AlphaFold Protein Structure DatabasePredicted protein structures from AlphaFold. 12InterProProtein families, domains and functional sites. 13Human Protein AtlasMap of human proteins in cells, tissues and organs.

Pathway & Interaction Databases

5 entries

Networks of reactions and interactions.

14KEGGDatabase of pathways, genes, genomes and chemical compounds. 15ReactomeCurated, peer-reviewed pathway database. 16STRINGProtein-protein interaction networks. 17WikiPathwaysCommunity-curated biological pathways. 18BioCycCollection of pathway and genome databases.

Variation, Expression & Literature

4 entries

Human variation, expression and publications.

19ClinVarArchive of relationships between human variants and phenotypes. 20gnomADAggregated human genome and exome variation data. 21GTEx PortalGene expression and regulation across human tissues. 22PubMedBiomedical literature search from the US National Library of Medicine.

About Biological Databases

6 entries

Reading on what the databases are and how they are organised.

23Biological Databases as a Global Critical Infrastructure 24Biological Databases — Springer Handbook of Bio-/Neuroinformatics 25Biological Database Assertions Using the Scientific Literaturebmcbioinformatics.biomedcentral.com 26Biological Sequence Databases — Springer 27List of Biological Databases — Wikipedia 28Biological Databases: An Overview and Future Perspective

Genome Technology

6 entries

Sequencing, editing and the Human Genome Project.

29Genome Technology Program — NHGRI 30Genetics Technology, Tools and Methods — GenomeWeb 31A Novel Technology for Genome-Editing a Broad Range of Mutations 32Will Genome Sequencing Bring Precision Medicine for All 33MSc in Genome Science and Technology — UBC 34Human Genome ProjectNHGRI overview of the Human Genome Project and its outcomes.

Gene Expression & Genetic Maps

6 entries

How genes are expressed and located on chromosomes.

35Gene Expression — Genome.gov Glossary 36Intro to Gene Expression (Central Dogma) — Khan Academy 37Gene Mapping — Wikipedia 38Genetic Linkage and Mapping — Khan Academy 39Gene Mapping (Genome.gov glossary)NHGRI definition of gene mapping. 40Metabolic Pathway — WikipediaThe chemical reaction networks that keep cells running, and how they're catalogued.

Related Pages

10 entries

Related directories on this site.

41BioinformaticsBioinformatics resources and tools. 42Medical InformaticsMedical informatics links. 43Research ResourcesResearch resources hub. 44CS Research LabsComputer science research labs. 45HealthcareHealthcare hub: IoMT, integration engines, medical informatics and AI. 46Agentic AI Platforms for Life SciencesAgentic AI platforms for pharma, biotech and medtech. 47Graph DatabasesGraph database systems. 48Python Libraries for Data ScientistsPython data science libraries. 49Data ScienceData science hub. 50Database Management SystemsDatabase management systems across relational, NoSQL and analytical engines.

Frequently Asked Questions

What are biological databases?

Biological databases are organised collections of data such as DNA and protein sequences, structures, pathways and variants that researchers use to look up and analyse biological information.

Which databases hold DNA sequences?

GenBank at NCBI, the European Nucleotide Archive and DDBJ together form the International Nucleotide Sequence Database Collaboration and exchange data daily.

Where do I find protein information?

UniProt for sequences and function, the Protein Data Bank for 3D structures and the AlphaFold database for predicted structures.

What happened to Pfam?

Pfam's standalone website has been retired and its content is now served through InterPro, which is listed here.

Where can I learn to use these resources?

EMBL-EBI and NCBI offer free tutorials, and the Bioinformatics page lists learning platforms and tools.