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.
Download preprint: 09dupsmcmc.pdf, 310Kb
Download from publisher: http://dx.doi.org/10.1007/978-3-642-04744-2_13
Related web 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 modified: 09.10.2009
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