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Reconstructing Histories of Complex Gene Clusters on a Phylogeny

  • Tomáš Vinař
  • Broňa Brejová
  • Giltae Song
  • Adam Siepel
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5817)

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. Supplementary materials are located at http://compbio.fmph.uniba.sk/suppl/09recombcg/

Keywords

Branch Length Atom Type Guide Tree Ancestral Sequence Segment Type 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Tomáš Vinař
    • 1
  • Broňa Brejová
    • 1
  • Giltae Song
    • 2
  • Adam Siepel
    • 3
  1. 1.Faculty of Mathematics, Physics and InformaticsComenius UniversityBratislavaSlovakia
  2. 2.Center for Comparative Genomics and Bioinformatics, 506B Wartik LabPenn State UniversityUniversity ParkUSA
  3. 3.Dept. of Biological Statistics and Comp. BiologyCornell UniversityIthacaUSA

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