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Seminar - Ruchira Datta

Speaker: Ruchira Datta
Title: PHOG phylogenomic orthology prediction
Time: Wednesday June 24 at 13.30
Place: M2.12

We present a new algorithm, PHOG phylogenomic orthology prediction, which is available as a web service through the PhyloFacts Phylogenomic Encyclopedias.

Ortholog detection is essential in functional annotation of genomes, with applications to phylogenetic tree construction, prediction of protein-protein interaction and other tasks. PHOG employs a novel algorithm to identify orthologs using 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. Predicted orthologs are linked to GO annotations, pathway information and biological literature.

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