On recovering syntenic blocks from comparative maps

Zhixiang Chen (), Bin Fu (), Minghui Jiang () and Binhai Zhu ()
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Zhixiang Chen: University of Texas–Pan American
Bin Fu: University of Texas–Pan American
Minghui Jiang: Utah State University
Binhai Zhu: Montana State University

Journal of Combinatorial Optimization, 2009, vol. 18, issue 3, No 6, 307-318

Abstract: 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.

Keywords: NP-completeness; Approximation algorithms; Bioinformatics (search for similar items in EconPapers)
Date: 2009
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DOI: 10.1007/s10878-009-9233-x

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