A practical guide to orthology resources

Un guide pratique des ressources en matière d'orthologie

Paul de Boissier (1) , Bianca Habermann (1)

1 IBDM - Institut de Biologie du Développement de Marseille

Many resources exist which collect information on orthologous genes and provide this information to the research community. However, the algorithms used to collect orthologs, the type of data available for analysis or download, the range of organisms included, as well as the user-friendliness vary greatly between different orthology databases. In this review, we present a practical guide to the best-known orthology resources: we here briefly discuss their algorithmic details, review their taxonomic coverage, and illustrate their user-friendliness. Moreover, we evaluate their capability to detect remotely conserved orthologs and to resolve inparalog relationships in gene families. Moreover, we test them for potential false-positive classification by using a multi-domain protein family with a complex evolutionary history. Finally, we assess the availability and ease of usage of orthology search engines offered by orthology database providers for local usage.

Mots clés: orthology; evolution; orthology resources; orthology

Domaines: Base de données [cs.DB]; Bio-informatique [q-bio.QM]

Paul de Boissier, Bianca Habermann. A practical guide to orthology resources. Pierre Pontarotti. Evolutionary Biology—A Transdisciplinary Approach, pp.41-77, 2020, 978-3-030-57245-7. ⟨10.1007/978-3-030-57246-4_3⟩. ⟨hal-03023036⟩