From: Koonin, Eugene (NIH/NLM/NCBI)
Sent: Friday, September 17, 2004 1:10 PM
To: 'ncbi-seminar@ncbi.nlm.nih.gov'; 'Oleg Rokhlenko'
Subject: Special seminar

Bldg. 38a, B2 conference room (NCBI library)
Tuesday Sept 21, 2 PM


Oleg Rokhlenko

Technion, Haifa, Israel


MetaPathwayHunter: a New Tool for the Alignment of Metabolic Pathways

Several genome-scale efforts are underway to reconstruct metabolic networks
for a variety of organisms.  As the resulting data accumulates, the need for
analysis tools increases. A notable requirement is a pathway alignment
finder that enables both the detection of conserved metabolic pathways among
different species as well as divergent metabolic pathways within a species.
When comparing two pathways, the tool should be powerful enough to take into
account both the pathway topology as well as the nodes'
labels (e.g. the enzymes they denote), and allow flexibility by matching
similar - rather than identical - pathways.

MetaPathwayHunter is a pathway alignment tool that, given a query pathway
and a collection of pathways, finds and reports all approximate occurrences
of the query in the collection, ranked by similarity and statistical
significance.  It is based on a novel, efficient graph matching algorithm
that extends the functionality of known techniques.  The program also
supports a visualization interface with which the alignment of two
homologous pathways can be graphically displayed.

We employed this tool to study the similarities and differences in the
metabolic networks of the bacterium Escherichia coli and the yeast
Saccharomyces cerevisiae, as represented in highly curated databases.
We reaffirmed that most known metabolic pathways common to both species are
conserved. Furthermore, we discovered a few intriguing relations between
pathways that provide insight into the evolution of metabolic pathways. We
conclude with a description of biologically meaningful meta-queries,
demonstrating the power and flexibility of our new tool in the analysis of
metabolic pathways. Joint work with Ron Pinter, Esti Yeger-Lotem and Michal
Ziv-Ukelson.


Eugene V. Koonin, PhD, Senior Investigator
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health
Bldg. 38A, Rm 5N503
Telephone 301-435-5913
Fax 301-435-5913