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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.
MSC:
68W05Nonnumerical algorithms
92C37Cell biology
92D10Genetics