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Computational Methods for the Analysis of Primate Mobile Elements

  • Richard Cordaux
  • Shurjo K. Sen
  • Miriam K. Konkel
  • Mark A. BatzerEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 628)

Abstract

Transposable elements (TE), defined as discrete pieces of DNA that can move from one site to another site in genomes, represent significant components of eukaryotic genomes, including primates. Comparative genome-wide analyses have revealed the considerable structural and functional impact of TE families on primate genomes. Insights into these questions have come in part from the development of computational methods that allow detailed and reliable identification, annotation, and evolutionary analyses of the many TE families that populate primate genomes. Here, we present an overview of these computational methods and describe efficient data mining strategies for providing a comprehensive picture of TE biology in newly available genome sequences.

Key words

Computational methods Transposable element Insertion Identification Classification Consensus sequence Subfamily Phylogenetic reconstruction Transpositional activity Primate Genome evolution 

Notes

Acknowledgments

Our research is supported by National Science Foundation BCS-0218338 (MAB) and EPS-0346411 (MAB), National Institutes of Health RO1 GM59290 (MAB) and PO1 AG022064 (MAB), and the State of Louisiana Board of Regents Support Fund (MAB). RC is supported by a Young Investigator ATIP award from the Centre National de la Recherche Scientifique (CNRS).

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Richard Cordaux
    • 1
  • Shurjo K. Sen
    • 2
  • Miriam K. Konkel
    • 2
  • Mark A. Batzer
    • 2
    Email author
  1. 1.Laboratoire Ecologie, Evolution et SymbioseCNRS UMR 6556, Universitè de PoitiersPoitiersFrance
  2. 2.Department of Biological Sciences, Biological Computation and Visualization CenterCenter for BioModular Multi-Scale Systems, Louisiana State UniversityBaton RougeUSA

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