OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation

Soheil Jahangiri-Tazehkand,Limsoon Wong,Changiz Eslahchi

doi:10.1016/j.gpb.2017.07.002

Soheil Jahangiri-Tazehkand, Limsoon Wong + Show 1 more

Open Access

https://doi.org/10.1016/j.gpb.2017.07.002

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Abstract

Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.

Highlights

Sequencing facilities are able to produce large amounts of gene and protein sequences in a short period of time
We propose OrthoGNC, a similarity-based method and a software that outputs highquality pairwise orthology relations based on gene neighborhood conservation
If in a round of orthology inference, OrthoGNC finds an ortholog for gene g in a strain, it does not look for another ortholog of gene g in the same strain in the subsequent rounds

Summary

Introduction

Sequencing facilities are able to produce large amounts of gene and protein sequences in a short period of time. Many complete genomes of organisms are available today for more in-depth comparative studies. Peer review under responsibility of Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. In comparative genomics is the identification of homologous and orthologous genes. Homologous genes (homologs) are originated from a gene in the last common ancestor. In 1970, Fitch classified homologs into orthologous and paralogous genes [1]. Orthologous genes (orthologs) are homologs that have evolved by speciation event in their last common ancestor. Paralogous genes (paralogs) are homologs that have evolved by gene duplication in their last common ancestor

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