Tractability and Approximability of Maximal Strip Recovery

  • Laurent Bulteau
  • Guillaume Fertin
  • Minghui Jiang
  • Irena Rusu
Conference paper

DOI: 10.1007/978-3-642-21458-5_29

Volume 6661 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Bulteau L., Fertin G., Jiang M., Rusu I. (2011) Tractability and Approximability of Maximal Strip Recovery. In: Giancarlo R., Manzini G. (eds) Combinatorial Pattern Matching. CPM 2011. Lecture Notes in Computer Science, vol 6661. Springer, Berlin, Heidelberg

Abstract

An essential task in comparative genomics is usually to decompose two or more genomes into synteny blocks, that is, segments of chromosomes with similar contents. In this paper, we study the Maximal Strip Recovery problem (MSR) [Zheng et al. 07], which aims at finding an optimal decomposition of a set of genomes into synteny blocks, amidst possible noise and ambiguities. We present a panel of new or improved FPT and approximation algorithms for the MSR problem and its variants. Our main results include the first FPT algorithm for the variant δ-gap-MSR-d, an FPT algorithm for CMSR-d and δ-gap-CMSR-d running in time O(2.360kpoly(nd)), where k is the number of markers or genes considered as erroneous, and a (d + 1.5)-approximation algorithm for CMSR-d and δ-gap-CMSR-d.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Laurent Bulteau
    • 1
  • Guillaume Fertin
    • 1
  • Minghui Jiang
    • 2
  • Irena Rusu
    • 1
  1. 1.Laboratoire d’Informatique de Nantes-Atlantique (LINA), UMR CNRS 6241Université de NantesNantes Cedex 3France
  2. 2.Department of Computer ScienceUtah State UniversityLoganUSA