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Genomic sorting with length-weighted reversals.

Authors: Pinter, Ron Y.; Skiena, Steven;

Genomic sorting with length-weighted reversals.

Abstract

Current algorithmic studies of genome rearrangement ignore the length of reversals (or inversions); rather, they only count their number. We introduce a new cost model in which the lengths of the reversed sequences play a role, allowing more flexibility in accounting for mutation phenomena. Our focus is on sorting unsigned (unoriented) permutations by reversals; since this problem remains difficult (NP-hard) in our new model, the best we can hope for are approximation results. We propose an efficient, novel algorithm that takes (a monotonic function f of) length into account as an optimization criterion and study its properties. Our results include an upper bound of O(fn lg2n) for any additive cost measure f on the cost of sorting any n-element permutation, and a guaranteed approximation ratio of O(lg2n) times optimal for sorting a given permutation. Our work poses some interesting questions to both biologists and computer scientists and suggests some new bioinformatic insights that are currently being studied.

Keywords

genome rearrangements, Chromosome Mapping, Computational Biology, length sensitive cost, Evolution, Molecular, Animals, Humans, Crossing Over, Genetic, sorting by reversal, Algorithms

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
10
Average
Top 10%
Average