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On recovering syntenic blocks from comparative maps

Author

Listed:
  • Zhixiang Chen

    (University of Texas–Pan American)

  • Bin Fu

    (University of Texas–Pan American)

  • Minghui Jiang

    (Utah State University)

  • Binhai Zhu

    (Montana State University)

Abstract

A genomic map is represented by a sequence of gene markers, and a gene marker can appear in several different genomic maps, in either positive or negative form. A strip (syntenic block) is a sequence of distinct markers that appears as subsequences in two or more maps, either directly or in reversed and negated form. Given two genomic maps G and H, the problem Maximal Strip Recovery (MSR) is to find two subsequences G′ and H′ of G and H, respectively, such that the total length of disjoint strips in G′ and H′ is maximized. Previously only a heuristic was provided for this problem, which does not guarantee finding the optimal solution, and it was unknown whether the problem is NP-hard or polynomially solvable. In this paper, we develop a factor-4 polynomial-time approximation algorithm for the problem, and show that several close variants of the problem are intractable.

Suggested Citation

  • Zhixiang Chen & Bin Fu & Minghui Jiang & Binhai Zhu, 2009. "On recovering syntenic blocks from comparative maps," Journal of Combinatorial Optimization, Springer, vol. 18(3), pages 307-318, October.
    • Handle: RePEc:spr:jcomop:v:18:y:2009:i:3:d:10.1007_s10878-009-9233-x
    DOI: 10.1007/s10878-009-9233-x
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    References listed on IDEAS

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    1. Erdong Chen & Linji Yang & Hao Yuan, 2007. "Improved algorithms for largest cardinality 2-interval pattern problem," Journal of Combinatorial Optimization, Springer, vol. 13(3), pages 263-275, April.
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