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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W84-9. doi: 10.1093/nar/gkp373. Epub 2009 May 12.

Berkeley PHOG: PhyloFacts orthology group prediction web server.

Author information

  • 1QB3 Institute, University of California, Berkeley, CA, USA. ruchira@berkeley.edu

Abstract

Ortholog detection is essential in functional annotation of genomes, with applications to phylogenetic tree construction, prediction of protein-protein interaction and other bioinformatics tasks. We present here the PHOG web server employing a novel algorithm to identify orthologs based on phylogenetic analysis. Results on a benchmark dataset from the TreeFam-A manually curated orthology database show that PHOG provides a combination of high recall and precision competitive with both InParanoid and OrthoMCL, and allows users to target different taxonomic distances and precision levels through the use of tree-distance thresholds. For instance, OrthoMCL-DB achieved 76% recall and 66% precision on this dataset; at a slightly higher precision (68%) PHOG achieves 10% higher recall (86%). InParanoid achieved 87% recall at 24% precision on this dataset, while a PHOG variant designed for high recall achieves 88% recall at 61% precision, increasing precision by 37% over InParanoid. PHOG is based on pre-computed trees in the PhyloFacts resource, and contains over 366 K orthology groups with a minimum of three species. Predicted orthologs are linked to GO annotations, pathway information and biological literature. The PHOG web server is available at http://phylofacts.berkeley.edu/orthologs/.

PMID:
19435885
[PubMed - indexed for MEDLINE]
PMCID:
PMC2703887
Free PMC Article

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