原创力文档Exact and Approximation Algorithms for Sorting By Reversals, With Application to Genome Rearrangement：（精确和近似算法排序的逆转,应用基因组重排）.pdfVIP
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Exact and approximation algorithms
for sorting by reversals with application
to genome rearrangement
y z
John Kececioglu David Sanko
Octob er revised February
Abstract Motivated by the problem in computational biology of reconstructing
the series of chromosome inversions by which one organism evolved from another
we consider the problem of computing the shortest series of reversals that trans
form one p ermutation to another The p ermutations describ e the order of genes
on corresp onding chromosomes and a reversal takes an arbitrary substring of
elements and reverses their order
For this problem we develop two algorithms a greedy approximation algorithm
that nds a solution provably close to optimal in O n 2 time and O n space for
an n element p ermutation and a branch and b ound exact algorithm that nds
an optimal solution in O mL n n time and O n 2 space where m is the size
of the branch and b ound search tree and L n n is the time to solve a linear
program of n variables and n constraints The greedy algorithm is the rst to
come within a constant factor of the optimum it guarantees a solution that uses
no more than twice the minimum numb er of reversals The lower and upp er
b ounds of the branch and b ound algorithm are a novel application of maximum
weight matchings shortest paths and linear programming
In a series of exp eriments we study the p erformance of an implementation
on random p ermutations and p ermutations generated by random reversals For
p ermutations
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