Identifying orthologs with OMA: A primer.

Monique Zahn-Zabal,Natasha M Glover,Christophe Dessimoz

doi:10.12688/f1000research.21508.1

Monique Zahn-Zabal, Natasha M Glover + Show 1 more

Open Access

https://doi.org/10.12688/f1000research.21508.1

Copy DOI

Abstract

The Orthologous Matrix (OMA) is a method and database that allows users to identify orthologs among many genomes. OMA provides three different types of orthologs: pairwise orthologs, OMA Groups and Hierarchical Orthologous Groups (HOGs). This Primer is organized in two parts. In the first part, we provide all the necessary background information to understand the concepts of orthology, how we infer them and the different subtypes of orthology in OMA, as well as what types of analyses they should be used for. In the second part, we describe protocols for using the OMA browser to find a specific gene and its various types of orthologs. By the end of the Primer, readers should be able to (i) understand homology and the different types of orthologs reported in OMA, (ii) understand the best type of orthologs to use for a particular analysis; (iii) find particular genes of interest in the OMA browser; and (iv) identify orthologs for a given gene. The data can be freely accessed from the OMA browser at https://omabrowser.org.

Highlights

Evolution is one of the fundamental principles of biology
In comparative genomics and phylogenetics, the fundamental concept of orthology relates “corresponding” genes in different species: orthologs are pairs of genes which have evolved from a single gene in the last common ancestor[1]
Methods on understanding orthology, we focus on i) the basic concepts of orthology, ii) defining the sub-types of orthology we infer in Orthologous Matrix (OMA), and iii) the key differences between the different types of orthologs, which can help to make a decision on what type to use for your own analyses

Summary

Introduction

A major concept in evolution is that of homology or the relationship between genes related by common ancestry From this general homologous relationship, pairs of genes might be classified in any of various sub-groups of homologs, including ortholog, co-ortholog, paralog, in-paralog, out-paralog, xenolog, or homoeolog, among others. A wide range of methods have been developed to infer orthologs, including PANTHER, OrthoInspector, InParanoid, and OrthoDB, among others (reviewed by Altenhoff[5]). This primer focuses on OMA (Orthologous MAtrix), a widely used method and database for inferring orthologs between species, and described the OMA Browser[6]

Methods

Discussion

Conclusion