Vinar, T., Brejova, B., Song, G., Siepel, A. (September 2010) Reconstructing histories of complex gene clusters on a phylogeny. J Comput Biol, 17 (9). pp. 1267-79. ISSN 1066-5277
Abstract
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. These 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.
Item Type: | Paper |
---|---|
Uncontrolled Keywords: | *Algorithms Animals Base Sequence *Evolution, Molecular Gene Duplication Genetic Speciation Genome Genomics/*methods Humans *Models, Genetic *Multigene Family *Phylogeny |
Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function |
CSHL Authors: | |
Communities: | CSHL labs > Siepel lab |
Depositing User: | Matt Covey |
Date: | September 2010 |
Date Deposited: | 13 Jan 2015 19:23 |
Last Modified: | 13 Jan 2015 19:23 |
Related URLs: | |
URI: | https://repository.cshl.edu/id/eprint/31112 |
Actions (login required)
Administrator's edit/view item |