The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

Adrian M Altenhoff,Klara Kaleb,Charles Stevenson,Jiao Long,Alex Warwick Vesztrocy,Henning Redestig,Tarcisio M De Farias,Karina Zile,David Dylus,Christophe Dessimoz,Gaston H Gonnet,Natasha M Glover,Clément-Marie Train

doi:10.1093/nar/gkx1019

Abstract

The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.

Highlights

Orthology, the formalization of the intuitive notion of ‘corresponding genes in different species’, is a cornerstone of genomics
Because orthologs are so important, a large number of methods and resources for their inference have been developed over the years, such as the COGs database [4], Inparanoid [5], OrthoMCL [6], Ensembl Compara [7], KEGG Orthology [8], PhylomeDb [9], OrthoDB [10], EggNOG [11], Microbial Genome Database (MBGD) [12], PLAZA [13] or Orthologous Matrix (OMA) [14]
D480 Nucleic Acids Research, 2018, Vol 46, Database issue set of genomes, we provide a function to retrieve, for a given subset of species, the most complete OMA groups

Summary

Introduction

The formalization of the intuitive notion of ‘corresponding genes in different species’, is a cornerstone of genomics (reviewed in 1). Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. We review some of the major new functionalities, including a viewer for hierarchical orthologous groups, domain annotations, a dotplot synteny viewer and improved programmatic accesses.

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Conclusion