Trapezoid graphs and generalizations, geometry and algorithms
Discrete Applied Mathematics
Chaining multiple-alignment fragments in sub-quadratic time
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Introduction to Algorithms
A small trip in the untranquil world of genomes
Theoretical Computer Science
Efficient chaining of seeds in ordered trees
Journal of Discrete Algorithms
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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.