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Stochastic Insertion-Deletion Processes and Statistical Sequence Alignment

In: Interacting Stochastic Systems

Author

Listed:
  • Dirk Metzler

    (Goethe-Universität, FB Biologie und Informatik)

  • Roland Fleißner

    (University of Idaho, Department of Mathematics)

  • Anton Wakolbinger

    (Goethe-Universität, FB Mathematik)

  • Arndt von Haeseler

    (Heinrich-Heine-Universität, Bioinformatik
    Forschungszentrum Jülich, John von Neumann-Institut für Computing (NIC), Forschungsgruppe Bioinformatik)

Abstract

Summary The reconstruction of the history of a set of sequences is a central problem in molecular evolutionary biology. Typically this history is summarized in a phylogenetic tree. In current practice the estimation of a phylogenetic tree is a two-step procedure: first a multiple alignment is computed and subsequently a phylogenetic tree is reconstructed, based on the alignment. However, it is well known that the alignment and the tree reconstruction problem are intertwined. Thus, it is of great interest to estimate alignment and tree simultaneously. We present here a stochastic framework for this joint estimation. We discuss a variant of the Thorne-Kishino-Felsenstein model, having equal rates of insertions and of deletions of sequence fragments, for $$\ell $$ ≥ 2 sequences related by a phylogenetic tree. Finally, we review novel approaches to tree reconstruction based on insertion-deletion models.

Suggested Citation

  • Dirk Metzler & Roland Fleißner & Anton Wakolbinger & Arndt von Haeseler, 2005. "Stochastic Insertion-Deletion Processes and Statistical Sequence Alignment," Springer Books, in: Jean-Dominique Deuschel & Andreas Greven (ed.), Interacting Stochastic Systems, pages 247-267, Springer.
    • Handle: RePEc:spr:sprchp:978-3-540-27110-9_11
    DOI: 10.1007/3-540-27110-4_11
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