IDEAS home Printed from https://ideas.repec.org/a/spr/jcomop/v16y2008i3d10.1007_s10878-007-9129-6.html
   My bibliography  Save this article

A new recombination lower bound and the minimum perfect phylogenetic forest problem

Author

Listed:
  • Yufeng Wu

    (University of Connecticut)

  • Dan Gusfield

    (University of California)

Abstract

Understanding recombination is a central problem in population genetics. In this paper, we address an established computational problem in this area: compute lower bounds on the minimum number of historical recombinations for generating a set of sequences (Hudson and Kaplan in Genetics 111, 147–164, 1985; Myers and Griffiths in Genetics 163, 375–394, 2003; Gusfield et al. in Discrete Appl. Math. 155, 806–830, 2007; Bafna and Bansal in IEEE/ACM Trans. Comput. Biol. Bioinf. 1, 78–90, 2004 and in J. Comput. Biol. 13, 501–521, 2006; Song et al. in Bioinformatics 421, i413–i244, 2005). In particular, we propose a new recombination lower bound: the forest bound. We show that the forest bound can be formulated as the minimum perfect phylogenetic forest problem, a natural extension to the classic binary perfect phylogeny problem, which may be of interests on its own. We then show that the forest bound is provably higher than the optimal haplotype bound (Myers and Griffiths in Genetics 163, 375–394, 2003), a very good lower bound in practice (Song et al. in Bioinformatics 421, i413–i422, 2005). We prove that, like several other lower bounds (Bafna and Bansal in J. Comput. Biol. 13, 501–521, 2006), computing the forest bound is NP-hard. Finally, we describe an integer linear programming (ILP) formulation that computes the forest bound precisely for certain range of data. Simulation results show that the forest bound may be useful in computing lower bounds for low quality data.

Suggested Citation

  • Yufeng Wu & Dan Gusfield, 2008. "A new recombination lower bound and the minimum perfect phylogenetic forest problem," Journal of Combinatorial Optimization, Springer, vol. 16(3), pages 229-247, October.
    • Handle: RePEc:spr:jcomop:v:16:y:2008:i:3:d:10.1007_s10878-007-9129-6
    DOI: 10.1007/s10878-007-9129-6
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s10878-007-9129-6
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1007/s10878-007-9129-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:jcomop:v:16:y:2008:i:3:d:10.1007_s10878-007-9129-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.