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Bioinformatics Resources on the Web

1. Major Data Submission Centers

  • NCBI (National Center for Biotechnology Information)
  • EBI (European Bioinformatics Institute)
  • RCBI/PDB (Research Collaboratory for Structural Bioinformatics)

2. Archival or Primary Databases

  • GenBank at NCBI
  • UNIPROT at EBI (previously SWISS-PROT and TrEMBL)
  • PDB  (Protein Data Bank) at  RCSB -Structural Database

3. Derived or Value-added Databases

    Sequence Databases

  • PROSITE (A database of protein profiles and patterns)
  • PRODOM (The PROtein DOMain 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

  • UCSC 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)

4. Useful Tools

  • BLAST (Pair-wise sequence alignment tools)
  • CLUSTALW (Multiple sequence alignment tool)
  • CD-HIT (Protein sequence clustering tool)
  • 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) (Example)
  • JALVIEW (Multiple sequence alignment viewer and editor)

5. Data Formats

6. Interesting Bioinformatics Resources


Suggested Reading


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