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Author Swenson, Krister M. ♦ Marron, Mark ♦ Earnest-Deyoung, Joel V. ♦ Moret, Bernard M E
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2008
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Computer programming, programs & data
Subject Keyword Evolution ♦ Duplications ♦ Inversions ♦ Pairwise distances ♦ Whole-genome data
Abstract As more and more genomes are sequenced, evolutionary biologists are becoming increasingly interested in evolution at the level of whole genomes, in scenarios in which the genome evolves through insertions, duplications, deletions, and movements of genes along its chromosomes. In the mathematical model pioneered by Sankoff and others, a unichromosomal genome is represented by a signed permutation of a multiset of genes; Hannenhalli and Pevzner showed that the edit distance between two signed permutations of the same set can be computed in polynomial time when all operations are inversions. El-Mabrouk extended that result to allow deletions and a limited form of insertions (which forbids duplications); in turn we extended it to compute a nearly optimal edit sequence between an arbitrary genome and the identity permutation. In this paper we generalize our approach to compute distances between two arbitrary genomes, but focus on approximating the true evolutionary distance rather than the edit distance. We present experimental results showing that our algorithm produces excellent estimates of the true evolutionary distance up to a (high) threshold of saturation; indeed, the distances thus produced are good enough to enable the simple neighbor-joining procedure to reconstruct our test trees with high accuracy.
ISSN 10846654
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2008-08-01
Publisher Place New York
e-ISSN 10846654
Journal Journal of Experimental Algorithmics (JEA)
Volume Number 12
Page Count 17
Starting Page 1
Ending Page 17

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Source: ACM Digital Library