A local chaining algorithm and its applications in comparative genomics

Abstract. Given fragments from multiple genomes, we will show how to find an optimal local chain of colinear non-overlapping fragments in sub-quadratic time, using methods from computational geometry. A variant of the algorithm finds all significant local chains of colinear nonoverlapping fragments. The local chaining algorithm can be used in a variety of problems in comparative genomics: The identification of regions of similarity (candidate regions of conserved synteny), the detection of genome rearrangements such as transpositions and inversions, and exon prediction.