Tomas Vinar, Brona Brejova, Giltae Song, Adam Siepel. Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny. Technical Report arXiv:0906.2635, arXiv.org, 2009.

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Abstract:

Clusters of genes that have evolved by repeated segmental duplication 
present difficult challenges throughout genomic analysis, from sequence 
assembly to functional analysis. Improved understanding of these clusters 
is of utmost importance, since they have been shown to be the source of 
evolutionary innovation, and have been linked to multiple diseases, 
including HIV and a variety of cancers. Previously, Zhang et al. (2008) 
developed an algorithm for reconstructing parsimonious evolutionary 
histories of such gene clusters, using only human genomic sequence data. 
In this paper, we propose a probabilistic model for the evolution of gene 
clusters 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 that our method 
will be useful in analyzing these valuable new data sets. 

Last update: 06/17/2009