Maximal Strip Recovery Problem with Gaps: Hardness and Approximation Algorithms

Abstract. Given two comparative maps, that is two sequences of markers each representing a genome, the Maximal Strip Recovery problem (MSR) asks to extract a largest sequence of markers from each map such that the two extracted sequences are decomposable into non-overlapping strips (or synteny blocks). This aims at dening a robust set of synteny blocks between dierent species, which is a key to understand the evolution process since their last common ancestor. In this paper, we add a fundamental constraint to the initial problem, which expresses the biologically sustained need to bound the number of intermediate (non-selected) markers between two consecutive markers in a strip. We therefore introduce the problem δ-gap-MSR, where δ is a (usually small) non-negative integer that upper bounds the number of non-selected markers between two consecutive markers in a strip. Depending on the nature of the comparative maps (i.e., with or without duplicates), we show that δ-gap-MSR is NP-co...

• Type: Conference
• Year: 2009
• Where: ISAAC
• Authors: Laurent Bulteau, Guillaume Fertin, Irena Rusu
• Keywords: Algorithms, Consecutive Markers, ISAAC 2009, Markers, Synteny Blocks