Tractability and Approximability of Maximal Strip Recovery

Abstract : An essential task in comparative genomics is usually to de- compose two or more genomes into synteny blocks, that is, segments of chromosomes with similar contents. In this paper, we study the Maxi- mal Strip Recovery problem (MSR) [Zheng et al. 07], which aims at nding an optimal decomposition of a set of genomes into synteny blocks, amidst possible noise and ambiguities. We present a panel of new or im- proved FPT and approximation algorithms for the MSR problem and its variants. Our main results include the rst FPT algorithm for the vari- ant -gap-MSR-d, an FPT algorithm for CMSR-d and -gap-CMSR-d running in time O(2:360kpoly(nd)), where k is the number of markers or genes considered as erroneous, and a (d + 1:5)-approximation algorithm for CMSR-d and -gap-CMSR-d.
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Communication dans un congrès
22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011), 2011, Palermo, Italy. Springer, LNCS (6661), pp.336-349, 2011, Lecture Notes in Computer Science
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Contributeur : Guillaume Fertin <>
Soumis le : mardi 5 juillet 2011 - 15:45:18
Dernière modification le : jeudi 5 avril 2018 - 10:36:48
Document(s) archivé(s) le : lundi 12 novembre 2012 - 10:10:44

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Laurent Bulteau, Guillaume Fertin, Minghui Jiang, Irena Rusu. Tractability and Approximability of Maximal Strip Recovery. 22nd Annual Symposium on Combinatorial Pattern Matching (CPM 2011), 2011, Palermo, Italy. Springer, LNCS (6661), pp.336-349, 2011, Lecture Notes in Computer Science. 〈hal-00606167〉

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