Format

Send to

Choose Destination
Nucleic Acids Res. 2011 Mar;39(5):e32. doi: 10.1093/nar/gkq953. Epub 2010 Dec 11.

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

Author information

1
Bioinformatics and Genomics Programme, Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Dr. Aiguader, 88. 08003, Barcelona, Spain.

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.

PMID:
21149260
PMCID:
PMC3061081
DOI:
10.1093/nar/gkq953
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center