On the Tractability of Maximal Strip Recovery

Abstract

Given two genomic maps G and H represented by a sequence of n gene markers, a strip (syntenic block) is a sequence of distinct markers of length at least two which appear as subsequences in the input maps, either directly or in reversed and negated form. 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 (or, conversely, the number of markers hence deleted, is minimized). Previously, besides some heuristic solutions, a factor-4 polynomial-time approximation is known for the MSR problem; moreover, several close variants of MSR, MSR-d (with d > 2 input maps), MSR-DU (with marker duplications) and MSR-WT (with markers weighted) are all shown to be NP-complete. Before this work, the complexity of the original MSR problem was left open. In this paper, we solve the open problem by showing that MSR is NP-complete, using a polynomial time reduction from One-in-Three 3SAT. We also solve the MSR problem and its variants exactly with FPT algorithms, i.e., showing that MSR is fixed-parameter tractable. Let k be the minimum number of markers deleted in various versions of MSR, the running time of our algorithms are O(22.73k n + n 2) for MSR, O(22.73k dn + dn 2) for MSR-d, and O(25.46k n + n 2) for MSR-DU.KeywordsConjunctive Normal FormTruth AssignmentDistinct MarkerSyntenic BlockClose VariantThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.