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Equivalog protein families in the TIGRFAMs database

Part 3. Proteomics

3.6. Proteome Families

Short Specialist Review

  1. Jeremy D. Selengut,
  2. Daniel H. Haft

Published Online: 15 JAN 2005

DOI: 10.1002/047001153X.g306305

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Selengut, J. D. and Haft, D. H. 2005. Equivalog protein families in the TIGRFAMs database. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.6:88.

Author Information

  1. The Institute for Genomic Research, Rockville, MD, USA

Publication History

  1. Published Online: 15 JAN 2005

Abstract

An equivalog is a family of proteins conserved in function since their last common ancestor. This term differs from the term ortholog, which is not limited to groups with conserved function but is strictly limited to speciation events (and excludes horizontal gene transfers). Hidden Markov Models (HMMs) are mathematical constructs representing multiple sequence alignments. The TIGRFAMs database includes a large number of HMMs that represent equivalog families. The great utility of these models is that a sequence scoring higher than a threshold value versus an equivalog has a very high likelihood of being a member of the family and sharing the same function. Equivalog HMMs are useful in automatic genome annotation. The information that is manually attached to a gene by an annotator is instead attached to the equivalog HMM. This is then used to transfer the information automatically to the appropriate genes. Furthermore, groups of equivalog HMMs can be linked together to create computable objects representing proteins that act together in a biological process (such as a metabolic pathway). Such compound objects can be used in metabolic reconstruction and applied to genomic sequence data even prior to annotation.

Keywords:

  • equivalog;
  • Markov;
  • HMM;
  • TIGRFAMs;
  • annotation;
  • genome;
  • bioinformatics;
  • homology;
  • metabolic reconstruction