A Local Chaining Algorithm and Its Applications in Comparative Genomics
نویسندگان
چکیده
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
منابع مشابه
Chaining Algorithms and Applications in Comparative Genomics
University of Ulm, Germany 1.1 Motivation: Comparison of Whole Genomes . . . . . . 1-1 1.2 Basic Definitions and Concepts . . . . . . . . . . . . . . . . . . . . . 1-4 1.3 A Global Chaining Algorithm without Gap Costs 1-5 The Basic Chaining Algorithm • Applications 1.4 Incorporating Gap Costs into the Algorithm . . . . . . 1-10 Costs in the L1 Metric • Costs in the L∞ Metric 1.5 Variations . . ...
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