Breakpoint graphs and ancestral genome reconstructions
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093-0404, USA
Abstract
Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.
Footnotes
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↵1 Corresponding author.
↵E-mail ppevzner{at}cs.ucsd.edu; fax (858) 534-7029.
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[Supplemental material is available online at www.genome.org.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.082784.108.
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- Received June 30, 2008.
- Accepted January 22, 2009.
- Copyright © 2009 by Cold Spring Harbor Laboratory Press
