Library of Congress Cataloging-in-Publication Data Ohlebusch, Enno.Advanced topics in term rewriting / Enno Ohlebusch. p. cm. Includes bibliographical references and index.1. Rewriting systems (Computer science) I. Title.
We developed new algorithms and a software tool 'Multiple Genome Aligner' (MGA for short) that efficiently computes multiple genome alignments of large, closely related DNA sequences. For example, it can align 85% percent of the complete genomes of six human adenoviruses (average length 35305 bp.) in 159 seconds. An alignment of 74% of the complete genomes of three of strains of E. coli (lengths: 5528445; 5498450; 4639221 approximately bp.) is produced in 30 minutes.
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(n log k n) time and O(n log 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 log log n and the space complexity by a factor log n. For the sum-of-pairs gap cost, our algorithm improves the time complexity of their algorithm by a factor log n log log n . 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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