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| HAL : hal-00700598, version 1 |
| DOI : 10.1016/j.tcs.2012.04.034 |
| Fiche détaillée |  Récupérer au format |
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| Theoretical Computer Science 440-441 (2012) 14-28 |
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| Tractability and approximability of maximal strip recovery |
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| Laurent Bulteau 1Guillaume Fertin 1 |
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| LINA-COMBI Collaboration(s) |
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| (22/05/2012) |
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| An essential task in comparative genomics is to decompose two or more genomes into synteny blocks that are segments of chromosomes with similar contents. Given a set of d genomic maps each containing the same n markers without duplicates, the problem MAXIMAL STRIP RECOVERY (MSR) aims at finding a decomposition of the genomic maps into synteny blocks (strips) of the maximum total length ', by deleting the minimum number k = n' of markers which are likely noise and ambiguities. In this paper, we present a collection of new or improved FPT and approximation algorithms for MSR and its variants. Our main results include a 2O(d ')poly(nd) time FPT algorithm for -gap-MSR-d, a 2:36kpoly(nd) time FPT algorithm for both CMSR-d and -gap-CMSR-d, and a (d+1:5)-approximation algorithm for both CMSR-d and -gap-CMSR-d. |
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| 1 : | Laboratoire d'Informatique de Nantes Atlantique (LINA) |
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CNRS : UMR6241 – Université de Nantes – École Nationale Supérieure des Mines - Nantes |
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| 2 : | Department of Computer Science Utah State University |
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Utah State University |
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| Department of Computer Science Utah State University |
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| Domaine | : | Informatique/Complexité Informatique/Bio-informatique Sciences du Vivant/Bio-Informatique, Biologie Systémique |
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| Bioinformatics – Comparative genomics – Synteny blocks – Approximation algorithms – Parameterized complexity |
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| Liste des fichiers attachés à ce document : | |||||
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| hal-00700598, version 1 | |
| http://hal.archives-ouvertes.fr/hal-00700598 | |
| oai:hal.archives-ouvertes.fr:hal-00700598 | |
| Contributeur : Guillaume Fertin | |
| Soumis le : Mercredi 23 Mai 2012, 15:02:34 | |
| Dernière modification le : Mercredi 23 Mai 2012, 15:19:44 | |
