Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
SIAM Journal on Computing
Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing
An Efficient Genetic Algorithm for Job Shop Scheduling Problems
Proceedings of the 6th International Conference on Genetic Algorithms
Finding All Common Intervals of k Permutations
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Efficient Bounds for Oriented Chromosome Inversion Distance
CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
Journal of Computer and System Sciences
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
The incompatible desiderata of gene cluster properties
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Individual gene cluster statistics in noisy maps
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Integer linear programs for discovering approximate gene clusters
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
The reversal median problem, common intervals, and mitochondrial gene orders
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
The statistical significance of max-gap clusters
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Software note: Gene teams: a new formalization of gene clusters for comparative genomics
Computational Biology and Chemistry
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Comparing gene orders in completely sequenced genomes is a standard approach to locate clusters of functionally associated genes. Often, gene orders are modeled as permutations. Given k permutations of n elements, a k-tuple of intervals of these permutations consisting of the same set of elements is called a common interval. We consider several problems related to common intervals in multiple genomes. We present an algorithm that finds all common intervals in a family of genomes, each of which might consist of several chromosomes. We present another algorithm that finds all common intervals in a family of circular permutations. A third algorithm finds all common intervals in signed permutations. We also investigate how to combine these approaches. All algorithms have optimal worst-case time complexity and use linear space.