Evolutionary history reconstruction for Mammalian complex gene clusters

Zhang, Y., Song, G., Vinar, T., Green, E. D., Siepel, A., Miller, W. (2009) Evolutionary history reconstruction for Mammalian complex gene clusters. J Comput Biol, 16 (8). pp. 1051-70. ISSN 1066-5277

URL: http://www.ncbi.nlm.nih.gov/pubmed/19645598
DOI: 10.1089/cmb.2009.0040

Abstract

Clusters of genes that evolved from single progenitors via repeated segmental duplications present significant challenges to the generation of a truly complete human genome sequence. Such clusters can confound both accurate sequence assembly and downstream computational analysis, yet they represent a hotbed of functional innovation, making them of extreme interest. We have developed an algorithm for reconstructing the evolutionary history of gene clusters using only human genomic sequence data, which allows the tempo of large-scale evolutionary events in human gene clusters to be estimated. We further propose an extension of the method to simultaneously reconstructing the evolutionary histories of orthologous gene clusters in multiple primates, which will facilitate primate comparative sequencing studies that aim to reconstruct their evolutionary history more fully.

Item Type: Paper
Uncontrolled Keywords: *Algorithms Animals *Evolution, Molecular Genomics/*methods Humans Markov Chains Models, Genetic *Multigene Family
Subjects: bioinformatics > computational biology
evolution
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date Deposited: 12 Jan 2015 19:31
Last Modified: 12 Jan 2015 19:31
PMCID: PMC2879273
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31117

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