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

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

• Kim MK
• Seol YJ
• Park HS
• Jang SH
• Shin HC
• Cho KH

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