Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps

Abstract

Chaining fragments is a crucial step in genome alignment. Existing chaining algorithms compute a maximum weighted chain with no overlaps allowed between adjacent fragments. In practice, using local alignments as fragments, instead of MEMs, generates frequent overlaps between fragments, due to combinatorial reasons and biological factors, i.e. variable tandem repeat structures that differ in number of copies between genomic sequences. In this paper, in order to raise this limitation, we formulate a novel definition of a chain, allowing overlaps proportional to the fragments lengths, and exhibit an efficient algorithm for computing such a maximum weighted chain. We tested our algorithm on a dataset composed of 694 genome couples and accounted for significant improvements in terms of coverage, while keeping the running times below reasonable limits.