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Annual International Conference on Research in Computational Molecular Biology

RECOMB 2006: Research in Computational Molecular Biology pp 265–280Cite as

Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3909))

Abstract

Micro-indels are small insertion or deletion events (indels) that occur during genome evolution. The study of micro-indels is important, both in order to better understand the underlying biological mechanisms, and also for improving the evolutionary models used in sequence alignment and phylogenetic analysis. The inference of micro-indels from multiple sequence alignments of related genomes poses a difficult computational problem, and is far more complicated than the related task of inferring the history of point mutations. We introduce a tree alignment based approach that is suitable for working with multiple genomes and that emphasizes the concept of indel history. By working with an appropriately restricted alignment model, we are able to propose an algorithm for inferring the optimal indel history of homologous sequences that is efficient for practical problems. Using data from the ENCODE project as well as related sequences from multiple primates, we are able to compare and contrast indel events in both coding and non-coding regions. The ability to work with multiple sequences allows us to refute a previous claim that indel rates are approximately fixed even when the mutation rate changes, and allows us to show that indel events are not neutral. In particular, we identify indel hotspots in the human genome.

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Author information

Authors and Affiliations

  1. Department of Mathematics, University of California, Berkeley, CA

    Sagi Snir & Lior Pachter

Authors
  1. Sagi Snir
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  2. Lior Pachter
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Editor information

Editors and Affiliations

  1. Georgia Institute of Technology and Università di Padova,  

    Alberto Apostolico

  2. Topic Chairs, P.O. Box

    Concettina Guerra

  3. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  4. University of California, San Diego, USA

    Pavel A. Pevzner

  5. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2006 Springer-Verlag Berlin Heidelberg

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Snir, S., Pachter, L. (2006). Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2006. Lecture Notes in Computer Science(), vol 3909. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11732990_23

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  • DOI: https://doi.org/10.1007/11732990_23

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-33295-4

  • Online ISBN: 978-3-540-33296-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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