Many of the databases listed below include interfaces for browsing and information access. Site tutorials are listed where available, and many sites may have tutorials not shown in this list. Software tools that may also incorporate these databases in some format can be found on the Software page.

Genotypes, Phenotypes, GWAS, Genetics

Resources for phenotype and genotype studies, genetics studies.

• dbGAP  Database of Genotype and Phenotype at NCBI. Currently, most studies need formal application through the IRB.

Genome Resources

With the final release of the human genome assembly, most of these browsers differ in interface, organization, and annotation. 

• UCSC Genome Browser - User-friendly browser: go from your sequence to a gene with BLAT, or browse chromosomes. Has a wealth of information mapped to the human genome including the ENCODE project.  [UCSC Genome Browser Online Tutorial/Training]
  
• GenBank  - Main page of the NCBI database, home of PubMed. More specific links in categories below. 
• Ensembl   The Ensembl genome browser (shares data with NCBI)
• EMBL - European Molecular Biology Laboratory.
• GDB - The Genome Database, an annotation resource with limited functionality
• CGAP The Cancer Genome Anatomy Project
• HCV Bioinformatics Resource Center  - Hepatitis C Viral Genome Database and other resources. UCSC (above) also has several viral species.

Protein Resources

Many protein resources can also be found in the genome repositories above. Those listed below are mostly specific for proteins. 

General protein databases 

• IPI - International Protein Index, an index that seeks to unify protein IDs across repositories.
• UniProt (formerly Swissprot/Trembl) at ExPASy - the Expert Protein Analysis System.
• iHOP - Information Hyperlinked Over Proteins. A "smart" tool that maps proteins to literature and back again. [Tutorial]

Proteomics Resources

• OPD: The Open Proteomics Database, which also gives some good links to other proteomics data sources. 

Protein Domains and 3D structure databases 

• PDB - Protein Data Bank: 3D structures of proteins; repository. Also can use Molecules To Go customizing tool.
• ExPASy protein structure links - List of protein domain and 3D databases, from the links page at ExPASy.

Antibody, Antigen, Immunology Databases

• Antibody Resource Page - Site with commercial suppliers, tools,  links to other antibody databases.
• Antibody/Epitope Registry Database -  Assists academic investigators in identifying viable antibodies for a variety of different research applications.
• HIV Molecular Immunology Database at LANL - Data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials.
• The Martin Group at UCL  - Many bioinformatics-meets-antibody resources in this lab's web pages.

Nucleotide and Microarray Databases

• GEO: The Gene Expression Omnibus at NCBI. Browse through data sets, see gene profiles across several dozen platforms, download microarray data when available.
• Stanford MicroArray Database  (Repository, Browseable)
• Oncomine - (Cancer Microarray Database)

Systems and Integrative Biology Databases

Resources such as protein-protein interaction networks, metabolic networks,  transcription and regulatory networks, and signaling networks. See a comprehensive listing at Pathguide.

Toxicogenomics, Chemical Genomics Databases

• CTD - The Comparative Toxicogenomics Database elucidates molecular mechanisms by which environmental chemicals affect human disease.
• Klotho - Biochemical compounds declarative db
• PubChem - PubChem provides information on the biological activities of small molecules