On Recovering Syntenic Blocks from Comparative Maps

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-complete 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.

• Type: Conference
• Year: 2008
• Where: COCOA
• Authors: Zhixiang Chen, Bin Fu, Minghui Jiang, Binhai Zhu
• Keywords: COCOA 2008, Discrete Geometry, Gene Marker, Genomic Maps, Problem Maximal Strip