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 non-overlapping 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. © Springer-Verlag Berlin Heidelberg 2003.
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CITATION STYLE
Abouelhoda, M. I., & Ohlebusch, E. (2003). A local chaining algorithm and its applications in comparative genomics. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag. https://doi.org/10.1007/978-3-540-39763-2_1
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