BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity

Hon Leong,Melvin Zhang

doi:10.1186/1752-0509-6-s1-s22

Abstract

BackgroundIdentifying corresponding genes (orthologs) in different species is an important step in genome-wide comparative analysis. In particular, one-to-one correspondences between genes in different species greatly simplify certain problems such as transfer of function annotation and genome rearrangement studies. Positional homologs are the direct descendants of a single ancestral gene in the most recent common ancestor and by definition form one-to-one correspondence.ResultsIn this work, we present a simple yet effective method (BBH-LS) for the identification of positional homologs from the comparative analysis of two genomes. Our BBH-LS method integrates sequence similarity and gene context similarity in order to get more accurate ortholog assignments. Specifically, BBH-LS applies the bidirectional best hit heuristic to a combination of sequence similarity and gene context similarity scores.ConclusionWe applied our method to the human, mouse, and rat genomes and found that BBH-LS produced the best results when using both sequence and gene context information equally. Compared to the state-of-the-art algorithms, such as MSOAR2, BBH-LS is able to identify more positional homologs with fewer false positives.

Highlights

Identifying corresponding genes in different species is an important step in genomewide comparative analysis
For each pair of genome, we compared the performance of bidirectional best hit (BBH)-LS, BBH using only normalized Smith-Waterman score (BBH), MSOAR2 [11], InParanoid 4.0 [17], OMA [21], Ensembl Compara [22], and OrthoMCL [14]
Positional homologs are the direct descendants of a single ancestral gene in the most recent common ancestor

Summary

Introduction

Identifying corresponding genes (orthologs) in different species is an important step in genomewide comparative analysis. One-to-one correspondences between genes in different species greatly simplify certain problems such as transfer of function annotation and genome rearrangement studies. Positional homologs are the direct descendants of a single ancestral gene in the most recent common ancestor and by definition form one-to-one correspondence. The identification of corresponding genes between different species is an important step in any genome-wide comparative analysis. One-to-one correspondences between genes in different species are preferred in certain applications such as transfer of function annotation [2] and genome rearrangement studies [3] as they greatly simplify subsequent analysis. For each gene in the MRCA, there is at most one direct descendant of the the concept of positional homologs, orthologs, and paralogs

Methods

Results

Conclusion