FACT: Functional annotation transfer between proteins with similar feature architectures

Background: The increasing number of sequenced genomes provides the basis for exploring the genetic and functional diversity within the tree of life. Only a tiny fraction of the encoded proteins undergoes a thorough experimental characterization. For the remainder, bioinformatics annotation tools are the only means to infer their function. Exploiting significant sequence similarities to already characterized proteins, commonly taken as evidence for homology, is the prevalent method to deduce functional equivalence. Such methods fail when homologs are too diverged, or when they have assumed a different function. Finally, due to convergent evolution, functional equivalence is not necessarily linked to common ancestry. Therefore complementary approaches are required to identify functional equivalents. Results: We present the Feature Architecture Comparison Tool http://www.cibiv.at/FACT to search for functionally equivalent proteins. FACT uses the similarity between feature architectures ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Tina Koestler, Arndt von Haeseler, Ingo Ebersberger
• Keywords: BMCBI 2010, Functional Equivalence, Functional Equivalents, Protein