Heuristics for the De Bruijn Graph Sequence Mapping Problem

Abstract

An important problem in Computational Biology is to map a sequencesinto a sequence graphG. One way to do this mapping is to find for a walk (or path)pinGsuch thatpspells a sequences′most similar tosand this problem is addressed by the Graph Sequence Mapping Problem --GSMP. In this article we consider theGSMPusing De Bruijn graph and we addressed by the De Bruijn Graph Sequence Mapping Problem --BSMP. Given a sequencesand a De Bruijn graphGk, withk≥ 2,BSMPconsists of finding a walkpinGksuch that the sequence spelled bypis the most similar tosgiven a distance, for example, edit distance.

The De Bruijn Graph Sequence Mapping Problem with Changes in the Graph

“…In a recently published article entitled Heuristic for the De Bruijn Mapping Problem [17], we dedicated ourselves to developing heuristics for Variant 1 (sequence alterations) of BSMP. However, in this new article, we focus on exploring Variant 2 (graph alterations) for BSMP.…”

“…Considering that we extensively explored this issue in our recent paper titled Heuristics for the De Bruijn Mapping Problem [15], specifically focusing on variant 1 for the De Bruijn graph, our current focus is on investigating variant 2, which involves changes only in the graph structure. The BSMP was previously addressed in the context of walks in an article titled On the Hardness of Sequence Alignment on De Bruijn Graphs [4], where Gibney et.…”