The quest for orthologs benchmark service and consensus calls in 2020

The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmar...

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Detalles Bibliográficos
Autores: Altenhoff, Adrian M, Garrayo Ventas, Javier, Consentino, Salvatore, Emms, David, Glover, Natasha M, Hernández Plaza, Ana, Nevers, Yannis, Szklarczyk, Damian, Fernández González, Jose María|||0000-0002-4806-5140, Codó, Laia, Gelpi, Josep|||0000-0002-0566-7723, Huertas Cepas, Jaime, Iwasaki, Wataru, Kelly, Steven, Lecompte, Odile, Muffato, Matthieu, Martín, María Jesús, Capella Gutiérrez, Salvador|||0000-0002-0309-604X, Thomas, Paul D., Sonnhammer, Erik, Dessimoz, Christophe, the Quest for Orthologs Consortium
Tipo de recurso: artículo
Fecha de publicación:2020
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/187596
Acceso en línea:https://hdl.handle.net/2117/187596
https://dx.doi.org/10.1093/nar/gkaa308
Access Level:acceso abierto
Palabra clave:Phylogeny
Proteins
Genomics
Comparative genomics
Molecular evolution
Orthologs
Quest for Orthologs consortium
Proteomes
Genòmica -- Informàtica
Filogènia
Proteïnes
Genòmica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
Descripción
Sumario:The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.

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