Heuristics for the De Bruijn Graph Sequence Mapping Problem

Abstract

AbstractIn computational biology, mapping a sequencesonto a sequence graphGis a significant challenge. One possible approach to addressing this problem is to identify a walkpinGthat spells a sequence which is most similar tos. This problem is known as the Graph Sequence Mapping Problem (GSMP). In this paper, we study an alternative problem formulation, namely the De Bruijn Graph Sequence Mapping Problem (BSMP), which can be stated as follows: given a sequencesand a De Bruijn graphGk(wherek≥ 2), find a walkpinGkthat spells a sequence which is most similar tosaccording to a distance metric. We present both exact algorithms and approximate distance heuristics for solving this problem, using edit distance as a criterion for measuring similarity.