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 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/.
QB3 Institute, University of California, Berkeley, CA, USA. ruchira@berkeley.edu
Ruchira S
RS
Datta
Christopher
C
Meacham
Bushra
B
Samad
Christoph
C
Neyer
Kimmen
K
Sjölander
D000465:Algorithms; D000818:Animals; D006801:Humans; D020407:Internet; D051379:Mice; D010802:Phylogeny; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface