Inferring Orthology and Paralogy.

Details

Serval ID
serval:BIB_062874BB14CB
Type
Article: article from journal or magazin.
Collection
Publications
Title
Inferring Orthology and Paralogy.
Journal
Methods in molecular biology
Author(s)
Altenhoff A.M., Glover N.M., Dessimoz C.
ISSN
1940-6029 (Electronic)
ISSN-L
1064-3745
Publication state
Published
Issued date
2019
Peer-reviewed
Oui
Volume
1910
Pages
149-175
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
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.
Keywords
Algorithms, Animals, Computational Biology/methods, Evolution, Molecular, Genome, Genomics/methods, Humans, Multigene Family, Phylogeny, Orthology, Orthology benchmarking, Paralogy, Tree reconciliation
Pubmed
Open Access
Yes
Create date
21/07/2019 16:39
Last modification date
11/01/2020 7:16
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