SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from Please contact us if you experience any problems.


This list contains links to some SUPERFAMILY related resources.

  • Julian Gough the original SUPERFAMILY author.

  • SCOP (Structural Classification of Proteins) is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships

  • ASTRAL provides sequences for each SCOP domain

  • SAM is a collection of software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis - used by us to build and score the SUPERFAMILY HMMs

  • PRC Profile Comparer for aligning and scoring two profile hidden Markov models - integrated into SUPERFAMILY sequence scoring

  • InterPro is a compendium of databases of protein families, domains and functional sites - includes SUPERFAMILY

  • Ensembl is a software system which produces and maintains automatic annotation on selected eukaryotic genomes - integrates SUPERFAMILY protein assignments

  • DAS is a communication protocol used to exchange biological sequence annotations - all SUPERFAMILY assignments are available through our protein DAS

  • TAIR (The Arabidopsis Information Resource) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana - integrates SUPERFAMILY assignments

  • DBD database of predicted transcription factors - uses a human curated set of SUPERFAMILY HMMs that represent DNA-binding domains

  • Meta II is a sequence analysis, and structure prediction server - SUPERFAMILY is one of the available prediction methods

  • SPiNE structural genomics project - SUPERFAMILY server is being used as part of the project

  • DOLOP analysis of predicted lipoproteins - uses SUPERFAMILY assignments

  • HIGH Human genome Immunoglobulin assignments - uses SUPERFAMILY assignments

  • VCN is a tool for visualising pre-clustered networks - previously used by SUPERFAMILY

  • Ranking Comparer compares occurrence of SCOP folds and superfamilies across genomes

  • Structure prediction meta-server provides access to various fold recognition, function prediction and local structure prediction methods - includes SUPERFAMILY method

  • LiveBench evaluation of the structure prediction servers - assessed SUPERFAMILY

  • EVA continously and automatically analyses protein structure prediction servers in 'real time' - assessed SUPERFAMILY

  • contains resources on Bioinformatics classified by categories

For information on how to link to the SUPERFAMILY web site, see the web services section.