General Bioinformatics Databases

Literature Search Engines

  • PubMed
    National Center for Biological Information database and tools.
  • PubChem
    Search engine provides information on the biological activities of small molecules. Search by compound (using name, synonyms or keywords), bioassay descriptions, chemical structure, etc.
  • Brenda
    Enzymes database.

Tools for Lab Work

Structural Databases


  • ExPASy
    ExPASy Proteomics Tool. A massive repository of analytical tools useful for all types of experimental work with proteins.
  • BLAST Basic Local Alignment Search Tool
    Protein and gene sequence homology alignments.
    Web-based sequence alignment tool.
    Analysis tools for predicting protein-protein interactions and biochemical pathways.


  • The SEED
    An annotation tool for detailed comparative genome analysis.
  • Kyoto Encyclopedia of Genes and Genomes
    A massive repository of protein function data, organized by type of data needed (such as pathway, orthology, genome, ligand).
  • J Craig Venter Institute
    Institute for genomic research.
  • ENTREZ Genome Project
    List of genomes being sequenced and their status: This is about as complete as we can find and provides useful links, status reports and contact information for various genome projects.
  • Gene Expression Omnibus
    A repository of data collected from microarray/gene expression profiling experiments.

 Biochemical Pathways Analysis


  • Phylogenetics Pipeline
    This is a useful website that allows one to go from a list of concatenated FASTA files to a phylogenetic tree, all in one, easy to use format.

Model Organisms Database