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Inferring Orthology and Paralogy

Altenhoff, AM; Glover, NM; Dessimoz, C; (2019) Inferring Orthology and Paralogy. Methods in Molecular Biology , 1910 pp. 149-175. 10.1007/978-1-4939-9074-0_5. Green open access

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Abstract

The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.

Type: Article
Title: Inferring Orthology and Paralogy
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1007/978-1-4939-9074-0_5
Publisher version: https://doi.org/10.1007/978-1-4939-9074-0_5
Language: English
Additional information: This chapter is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.
Keywords: Orthology, Paralogy, Tree reconciliation, Orthology benchmarking
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.ucl.ac.uk/id/eprint/10078014
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