From: Jothi, Raja (NIH/NLM)
Sent: Tuesday, September 06, 2005 10:50 AM
To: NLM/NCBI List ncbi-seminar
Subject: In 10 minutes: First Autumn 2005 NCBI seminar; 09/06/2005 11AM


Speaker: Raja Jothi
Time 11:00 AM
Place: Bldg 38a B2; NCBI library 

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A new phylogenetic approach to delineate ortholgous groups

Determining orthology relationship among genes across multiple genomes
is an important problem in the post-genomic era. Identifying orthologous
genes can not only help predict functional annotations for newly
sequenced or poorly characterized genomes, but can also help predict new
protein-protein interactions. Unfortunately, determining orthology
relation through computational methods is not straightforward due to the
presence of paralogs. Traditional approaches have relied on pairwise
sequence comparisons to construct graphs, which were then partitioned
into putative clusters of ortholgous groups. These methods do not
attempt to preserve the non-transitivity and hierarchic nature of the
orthology relation. We propose a new method, COCO-CL, for hierarchical
divisive (top-down) clustering of homology relations, and identification
of orthologous groups of genes. Unlike previous approaches, which are
based on pairwise sequence comparisons, our method explores the
correlation of evolutionary histories of individual genes in a more
global context, and does not assume that the species tree or the gene
tree is known. Our approach does not rely on e-value cut-offs, and is
independent of phylogenetic tree construction methods. Our method can be
used to delineate orthology/paralogy relation for a given set of
homologous proteins or as a refiner that removes putative out-paralogs
from clusters computed using a more inclusive approach. In particular,
without using the species tree information, our method identifies
putative duplication events in gene families. 
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