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Bioinformatics Advance Access originally published online on January 22, 2009
Bioinformatics 2009 25(6):729-735; doi:10.1093/bioinformatics/btp048
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SIMPRO: simple protein homology detection method by using indirect signals

Inkyung Jung 1 and Dongsup Kim 1,2,*

1Department of Bio and Brain Engineering and 2KAIST Institute for BioCentury, KAIST, Daejeon 305-701, South Korea

*To whom correspondence should be addressed.


  Abstract

Motivation: Detecting homologous proteins is one of the fundamental problems in computational biology. Many tools to solve this problem have been developed, but development of a simple, effective and generally applicable method is still desirable.

Results: We propose a simple but effective information retrieval approach, named SIMPRO, to identify homology relationship between proteins. The key idea of our approach is that by accumulating and comparing indirect signals from conventional homology search methods, the search sensitivity can be increased. We tested the idea on the problem of detecting homology relationship between Pfam families, as well as detecting structural homologs based on SCOP, and found that our method achieved significant improvement. Our results indicate that simple manipulation of conventional homology search outputs by SIMPRO algorithm can remarkably improve homology search accuracy.

Contact: kds{at}kaist.ac.kr

Associated Editor: Burkhard Rost

Received on November 18, 2008; revised on January 2, 2009; accepted on January 20, 2009

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