WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Journal of Discrete Algorithms
Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computing Common Intervals of $K$ Permutations, with Applications to Modular Decomposition of Graphs
SIAM Journal on Discrete Mathematics
Gene Team Tree: A Compact Representation of All Gene Teams
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Computation of median gene clusters
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
The incompatible desiderata of gene cluster properties
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
Using PQ trees for comparative genomics
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Consistency of sequence-based gene clusters
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
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In this paper, we study the problem of efficiently finding gene clusters formalized by nested common intervals between two genomes represented either as permutations or as sequences. Considering permutations, we give several algorithms whose running time depends on the size of the actual output rather than the output in the worst case. Indeed, we first provide a straightforward O (n 3) time algorithm for finding all nested common intervals. We reduce this complexity by providing an O (n 2) time algorithm computing an irredundant output. Finally, we show, by providing a third algorithm, that finding only the maximal nested common intervals can be done in linear time. Considering sequences, we provide solutions (modifications of previously defined algorithms and a new algorithm) for different variants of the problem, depending on the treatment one wants to apply to duplicated genes.