SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny

Nucleic Acids Res. 2009 Jan;37(Database issue):D380-6. doi: 10.1093/nar/gkn762. Epub 2008 Nov 26.


SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at Hidden Markov models based on Structural Classification of Proteins (SCOP) domain definitions at the superfamily level are used to provide structural annotation. We recently produced a new model library based on SCOP 1.73. Family level assignments are also available. From the web site users can submit sequences for SCOP domain classification; search for keywords such as superfamilies, families, organism names, models and sequence identifiers; find over- and underrepresented families or superfamilies within a genome relative to other genomes or groups of genomes; compare domain architectures across selections of genomes and finally build multiple sequence alignments between Protein Data Bank (PDB), genomic and custom sequences. Recent extensions to the database include InterPro abstracts and Gene Ontology terms for superfamiles, taxonomic visualization of the distribution of families across the tree of life, searches for functionally similar domain architectures and phylogenetic trees. The database, models and associated scripts are available for download from the ftp site.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computer Graphics
  • Databases, Protein*
  • Genomics
  • Humans
  • Phylogeny
  • Protein Structure, Tertiary* / genetics
  • Proteins / classification
  • Proteins / genetics*
  • Sequence Analysis, DNA
  • Sequence Analysis, Protein


  • Proteins