Zahn-Zabal, M;
Dessimoz, C;
Glover, N;
(2020)
Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved].
F1000Research
, 9
, Article 27. 10.12688/f1000research.21508.1.
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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 .
| Type: | Article |
|---|---|
| Title: | Identifying orthologs with OMA: A primer [version 1; peer review: 2 approved] |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.12688/f1000research.21508.1 |
| Publisher version: | http://dx.doi.org/10.12688/f1000research.21508.1 |
| Language: | English |
| Additional information: | © 2020 Zahn-Zabal M et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/). |
| Keywords: | OMA, Orthologous Matrix, orthology, phylogenetics, Hierarchical orthologous groups, Comparative genomics |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10090166 |
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