SIMPRO: simple protein homology detection method by using indirect signals

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.