Berkeley PHOG: PhyloFacts orthology group prediction web server

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 phylogene...

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Bibliographic Details
Published in:Nucleic acids research 2009-07, Vol.37 (suppl-2), p.W84-W89
Main Authors: Datta, Ruchira S, Meacham, Christopher, Samad, Bushra, Neyer, Christoph, Sjölander, Kimmen
Format: Article
Language:English
Subjects:
Algorithms
Animals
Humans
Internet
Mice
Phylogeny
Reproducibility of Results
Sequence Analysis, Protein
Software
User-Computer Interface
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Summary: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/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkp373