MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score

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• dc.contributor.author Pryszcz, Leszek Piotr, 1985-ca
• dc.contributor.author Huerta Cepas, Jaimeca
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
• dc.date.accessioned 2015-09-28T11:47:12Z
• dc.date.available 2015-09-28T11:47:12Z
• dc.date.issued 2011ca
• dc.description.abstract Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, the large computational cost associated to these analyses is a limiting factor that often prevents its use at genomic scales. Recently, several projects have addressed the reconstruction of large collections of high-quality phylogenetic trees from which orthology and paralogy relationships can be inferred. This provides us with the opportunity to infer the evolutionary relationships of genes from multiple, independent, phylogenetic trees. Using such strategy, we combine phylogenetic information derived from different databases, to predict orthology and paralogy relationships for 4.1 million proteins in 829 fully sequenced genomes. We show that the number of independent sources from which a prediction is made, as well as the level of consistency across predictions, can be used as reliable confidence scores. A webserver has been developed to easily access these data (http://orthology.phylomedb.org), which provides users with a global repository of phylogeny-based orthology and paralogy predictions.
• dc.description.sponsorship This work was supported by La Caixa pre-doctoral fellowship to L.P.; partial support by a grant from the Spanish Ministry of Science (BFU2009-09168) for T.G.’s research. Funding for open access charge: Spanish Ministry of Science (BFU2009-09168)
• dc.format.mimetype application/pdfca
• dc.identifier.citation Pryszcz LP, Huerta-Cepas J, Gabaldón T. MetaPhOrs: orthology and paralogy/npredictions from multiple phylogenetic evidence using a consistency-based/nconfidence score. Nucleic Acids Res. 2011 Mar;39(5):e32. DOI: 10.1093/nar/gkq953ca
• dc.identifier.doi http://dx.doi.org/10.1093/nar/gkq953
• dc.identifier.issn 0305-1048ca
• dc.identifier.uri http://hdl.handle.net/10230/24771
• dc.language.iso engca
• dc.publisher Oxford University Pressca
• dc.relation.ispartof Nucleic Acids Research. 2011 Mar;39(5):e32
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009-09168
• dc.rights © 2011 Leszek Piotr Pryszcz et al. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution Licenseca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by-nc/2.5
• dc.subject.other Genòmica
• dc.subject.other Filogènia
• dc.title MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence scoreca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca