Major Data Submission Centers
- NCBI (National Center for Biotechnology Information)
- EBI (European Bioinformatics Institute)
- RCBI/PDB (Research Collaboratory for Structural Bioinformatics)
Archival or Primary Databases
- GenBank at NCBI
- UNIPROT at EBI (previously SWISS-PROT and TrEMBL)
- PDB (Protein Data Bank) at RCSB -Structural Database
Derived or Value-added Databases
Sequence Databases
- PROSITE (A database of protein profiles and patterns)
- PFAM (Protein families database of alignments and HMMs)
- BLOCKS (Blocks WWW Server obtained from PROSITE)
- INTERPRO (Integrated Resource of Protein Domains and Functional Sites)
- Integr8 (Integrated browser to access complete genomes and proteomes at EBI)
Structure Databases
- CATH (Class Architecture, Topology & Homologous super family)
- SCOP (Structural Classification of Proteins)
- FSSP (Fold classification based on Structure-Structure alignment of Proteins)
- HSSP (A database of Homology-derived Secondary Structure of Proteins)
- HOMSTRAD (Homologous Structure Alignment Database)
- DSSP (Database of Secondary Structure Assignments)
- VAST (Vector Alignment Search Tool)
Specialized Databases/Web Resources
- UCSC Genome Browser
- Ensembl Genome Browser
- GO (The Gene Ontology)
- KEGG (Kyoto Encyclopedia of Genes and Genomes)
- OMIM (Online Mendelian Inheritance in Man)
- ENZYME (Enzyme Nomenclature Database)
- BRENDA (Comprehensive Enzyme Database)
- PMD (Protein Mutant Database)
- COG (Clusters of Orthologous Groups of proteins)
- DIP (Database of Interacting proteins)
Useful Tools
- BLAST (Pair-wise sequence alignment tools)
- CLUSTALW (Multiple sequence alignment tool)
- CD-HIT (Protein sequence clustering tool)
- PROFILEMAKE (Builds profiles for sequence families)
- HMMER (Software suite for sequence analysis using HMMs)
- PHYLIP (Software suite for phylogenetic analysis)
- PIPMAKER (Software suite for sequence comparison)
- MVIEW (Multiple sequence alignment viewer)
- JALVIEW (Multiple sequence alignment viewer and editor)
Data Formats
Interesting Bioinformatics Resources
- ExPASy Tools
- Amos' WWW links
- Genamics.com
- Colorbasepair.com
- Bioinformatics education at NCBI
- Biology Workbench at SDSC