Nucleic Acids Research Advance Access originally published online on May 12, 2009
Nucleic Acids Research 2009 37(Web Server issue):W84-W89; doi:10.1093/nar/gkp373
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W84-W89
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Berkeley PHOG: PhyloFacts orthology group prediction web server
1QB3 Institute, 2Department of Bioengineering and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
*To whom correspondence should be addressed. Tel: +1 510 642 6642; Fax: +1 510 642 5835; Email: ruchira{at}berkeley.edu
Received March 3, 2009. Revised April 22, 2009. Accepted April 24, 2009.
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/.
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