Useful Links

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)
  • PRODOM (ThePROteinDOMain Database-built from UNIPROT)
  • 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

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


Suggested Reading