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Chaining algorithms for multiple genome comparison. (English) Zbl 1110.68541
Summary: Given n fragments from k>2 genomes, Myers and Miller showed how to find an optimal global chain of colinear non-overlapping fragments in O(nlog k n) time and O(nlog k-1 n) space. For gap costs in the L 1 -metric, we reduce the time complexity of their algorithm by a factor log 2 n loglogn and the space complexity by a factor logn. For the sum-of-pairs gap cost, our algorithm improves the time complexity of their algorithm by a factor logn loglogn. A variant of our algorithm finds all significant local chains of colinear non-overlapping fragments. These chaining algorithms can be used in a variety of problems in comparative genomics: the computation of global alignments of complete genomes, the identification of regions of similarity (candidate regions of conserved synteny), the detection of genome rearrangements, and exon prediction.
68W05Nonnumerical algorithms
92C37Cell biology