From: Koonin, Eugene (NIH/NLM/NCBI)
Sent: Monday, August 29, 2005 8:21 PM
To: NLM/NCBI List ncbi-seminar
Cc: 'Firas Swidan'
Subject: Seminar Sept 27

Tuesday, September 27, 3 PM
Bldg. 38A, B2 conference room


Firas Swidan

The Technion, Haifa, Israel


An Integrative Method for Accurate Genome Mapping

In this talk I will present MAGIC, (a rearrangement of) an Integrative and
Accurate tool for Comparative Genome Mapping. The tool consists of two
phases: a preprocessing phase for identifying "maximal similar segments",
and a mapping phase for clustering the similar segments into
rearrangement-free regions while handling duplications.
MAGIC's preprocessing phase differs from previous work as it attempts to
build a comprehensive table of verified maximal similar segments, i.e.,
segments whose global alignment is free of long gaps.  MAGIC's mapping phase
is based on a novel and biologically intuitive clustering approach which is
capable of handling duplications, identifying orthologs and paralogs, as
well as classifying paralogs. The clustering integrates information from
several sources, systematically filtering extraneous insertions.  Our
improvements allow a comprehensive study of the diversity of genetic
repertoires resulting from large-scale mutations, i.e., indel mutations,
duplications, and transposable and phagic elements. The strength of our
method is demonstrated by the detailed statistics computed for each type of
these large-scale mutations. We have applied our particular implementation
to a genome-wide comparison of 10 pairs of prokaryotic genomes spanning
different branches of the tree of life. MAGIC enables, for the first time,
to analyze the different forces shaping these genomes, and to show that
horizontal gene transfer and large deletions affect genome evolution
significantly more than duplications. Furthermore, we used the method to
investigate the controversial Nadeau-Taylor model and showed - unexpectedly
- a good fit between the model's prediction and observed data in most cases.




Eugene V. Koonin, PhD, Senior Investigator
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health
Bethesda, MD 20894
Telephone 301-435-5913
Fax 301-435-7794