Genomics Inform.  2009 Sep;7(3):141-147.

A New Approach to Find Orthologous Proteins Using Sequence and Protein-Protein Interaction Similarity

Affiliations
  • 1Department of Bioinformatics and CAMDRC, Soongsil University, Seoul 156-743, Korea. chokh@ssu.ac.kr
  • 2Research Planning & Information Div., National Institute of Agricultural Biotechnology, RDA, Suwon 441-707, Korea.
  • 3Department of Computer Science, Ewha Womans University, Seoul 120-750, Korea.

Abstract

Developed proteome-scale ortholog and paralog prediction methods are mainly based on sequence similarity. However, it is known that even the closest BLAST hit often does not mean the closest neighbor. For this reason, we added conserved interaction information to find orthologs. We propose a genome-scale, automated ortholog prediction method, named OrthoInterBlast. The method is based on both sequence and interaction similarity. When we applied this method to fly and yeast, 17% of the ortholog candidates were different compared with the results of Inparanoid. By adding protein-protein interaction information, proteins that have low sequence similarity still can be selected as orthologs, which can not be easily detected by sequence homology alone.

Keyword

interolog; ortholog; protein-protein interaction

MeSH Terms

Diptera
Proteins
Sequence Homology
Yeasts
Proteins
Full Text Links
  • GNI
Actions
Cited
CITED
export Copy
Close
Share
  • Twitter
  • Facebook
Similar articles
Copyright © 2022 by Korean Association of Medical Journal Editors. All rights reserved.     E-mail: koreamed@kamje.or.kr