Chaining algorithms for multiple genome comparison |
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Authors: | Mohamed Ibrahim Abouelhoda Enno Ohlebusch |
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Affiliation: | Faculty of Computer Science, University of Ulm, 89069 Ulm, Germany |
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Abstract: | 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(nlogkn) time and O(nlogk−1n) space. For gap costs in the L1-metric, we reduce the time complexity of their algorithm by a factor 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 . 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. |
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Keywords: | Fragment-chaining algorithms Multiple alignment Comparative genomics Range maximum query |
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