Tomas Vinar, Brona Brejova, Giltae Song, Adam Siepel. Reconstructing Histories of Complex Gene Clusters on a Phylogeny. In F. D. Ciccarelli, I. Miklos, ed., Comparative Genomics, International Workshop (RECOMB-CG), 5817 volume of Lecture Notes in Bioinformatics, pp. 150-163, Budapest, September 2009. Springer.

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Download from publisher: http://dx.doi.org/10.1007/978-3-642-04744-2_13

Related www page: http://compbio.fmph.uniba.sk/suppl/09recombcg/

Bibliography entry: BibTeX

See also: early version

Abstract:

Clusters of genes that have evolved by repeated segmental duplication 
present difficult challenges throughout genomic analysis, from sequence 
assembly to functional analysis. The gene clusters are one of the major 
sources of evolutionary innovation, and they are linked to multiple 
diseases, including HIV and a variety of cancers. Understanding their 
evolutionary histories is a key to the application of comparative genomics 
methods in these regions of the genome. We propose a
probabilistic model of gene cluster evolution on a phylogeny, and an MCMC 
algorithm for reconstruction of duplication histories from genomic sequences 
in multiple species. Several projects are underway to obtain high quality 
BAC-based assemblies of duplicated clusters in multiple species, and we 
anticipate use of our methods in their analysis.

Last update: 10/09/2009