Subject: | Identifying conserved gene clusters in the presense of orthologous groups |
Presenter: | Baharak Rastegari |
Paper: | " Identifying conserved gene clusters in the presense of orthologous groups " |
  | by X. He and M.H. Goldwasser |
Abstract |
Identifying conserved gene clusters in the presense of orthologous groups
Current biological evidence suggests a correlation between the function
and the position of genes in chromosomes. Examples include operon
structure in prokaryotic genomes and similar expression patterns of
neighboring genes in some eukaryotic genomes. In this paper, we present a
new model and algorithm for identifying conserved gene clusters from
pairwise genome comparison. This generalizes a recent model called "gene
teams." A gene team is a set of orthologous genes that appear in two or
more species, possibly in a different order yet with the distance of
adjacent genes in the team for each chromosome always no more than a
certain threshold. We remove the constraint in the original model that
each gene must have a unique copy in the chromosomes, and thus allow the
analysis on complex prokaryotic or eukaryotic genomes with extensive
paralogs. Our algorithm runs in O(mn) time and uses O(m+n) space, where m
and n are the number of common genes in each chromosomes. We used this
approach to study two bacterial genomes, E. coli and B. subtilis and
successfully identified 85 conserved clusters, including clusters
containing uncharacterized genes and a large cluster consisting of 21
ribosomal proteins. Our implementation is publicly available at
http://euler.slu.edu/~goldwasser/cogteams/.
Reference:
X. He and M.H. Goldwasser, "Identifying conserved gene clusters in the
presense of orthologous groups", In RECOMB 2004, pp 272-280.
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