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ALGORITHMICA
2011
8 years 9 months ago
Common Intervals of Multiple Permutations
Abstract 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 present an algorith...
Steffen Heber, Richard Mayr, Jens Stoye
WABI
2001
Springer
138views Bioinformatics» more  WABI 2001»
9 years 6 months ago
Algorithms for Finding Gene Clusters
Abstract. Comparing gene orders in completely sequenced genomes is a standard approach to locate clusters of functionally associated genes. Often, gene orders are modeled as permut...
Steffen Heber, Jens Stoye
CPM
2004
Springer
108views Combinatorics» more  CPM 2004»
9 years 7 months ago
Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences
A popular approach in comparative genomics is to locate groups or clusters of orthologous genes in multiple genomes and to postulate functional association between the genes contai...
Thomas Schmidt, Jens Stoye
ESA
2005
Springer
131views Algorithms» more  ESA 2005»
9 years 8 months ago
Computing Common Intervals of K Permutations, with Applications to Modular Decomposition of Graphs
We introduce a new way to compute common intervals of K permutations based on a very simple and general notion of generators of common intervals. This formalism leads to simple an...
Anne Bergeron, Cedric Chauve, Fabien de Montgolfie...
CPM
2009
Springer
189views Combinatorics» more  CPM 2009»
9 years 9 months ago
Average-Case Analysis of Perfect Sorting by Reversals
A sequence of reversals that takes a signed permutation to the identity is perfect if it preserves all common intervals between the permutation and the identity. The problem of com...
Mathilde Bouvel, Cedric Chauve, Marni Mishna, Domi...
RECOMB
2006
Springer
10 years 2 months ago
Inferring Positional Homologs with Common Intervals of Sequences
Inferring orthologous and paralogous genes is an important problem in whole genomes comparisons, both for functional or evolutionary studies. In this paper, we introduce a new appr...
Guillaume Blin, Annie Chateau, Cedric Chauve, Yann...
RECOMB
2008
Springer
10 years 2 months ago
Perfect DCJ Rearrangement
We study the problem of transforming a multichromosomal genome into another using Double-Cut-and-Join (DCJ) operations. We introduce the notion of DCJ scenario that does not break ...
Sèverine Bérard, Annie Chateau, Cedr...
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