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COMMUNICATIONS IN INFORMATION AND SYSTEMS c 2010 International Press Vol. 10, No. 1, pp. 1-22, 2010 001
 

Summary: COMMUNICATIONS IN INFORMATION AND SYSTEMS c 2010 International Press
Vol. 10, No. 1, pp. 1-22, 2010 001
DECODING THE GENOMIC ARCHITECTURE OF MAMMALIAN
AND PLANT GENOMES: SYNTENY BLOCKS AND LARGE-SCALE
DUPLICATIONS
QIAN PENG¶, MAX A. ALEKSEYEV, GLENN TESLER§, AND PAVEL A. PEVZNER¶
Abstract. Motivation: The existing synteny block reconstruction algorithms use anchors (e.g.,
orthologous genes) shared over all genomes to construct the synteny blocks for multiple genomes.
This approach, while efficient for a few genomes, cannot be scaled to address the need to construct
synteny blocks in many mammalian genomes that are currently being sequenced. The problem is
that the number of anchors shared among all genomes quickly decreases with the increase in the
number of genomes. Another problem is that many genomes (plant genomes in particular) had
extensive duplications, which makes decoding of genomic architecture and rearrangement analysis in
plants difficult. The existing synteny block generation algorithms in plants do not address the issue
of generating non-overlapping synteny blocks suitable for analyzing rearrangements and evolution
history of duplications.
Results: In this paper we present a new synteny block generation algorithm based on the A-
Bruijn graph framework that overcomes these difficulties. We applied our algorithm to derive non-
overlapping synteny blocks in Arabidopsis thaliana. We also generalized this approach to synteny
block generation for multiple genomes. The algorithm was applied to human-mouse-rat-dog-chicken

  

Source: Alekseyev, Max - Department of Computer Science and Engineering, University of South Carolina

 

Collections: Biotechnology; Computer Technologies and Information Sciences