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| HAL: hal-00417728, version 1 |
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| ACM/IEEE Trans. Computational Biology and Bioinformatics 4, 4 (2007) 535-543 |
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| Exemplar Longest Common Subsequence |
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| Paola Bonizzoni 1Gianluca Della Vedova 2 |
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| (2007) |
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| In this paper, we investigate the computational and approximation complexity of the Exemplar Longest Common Subsequence of a set of sequences (ELCS problem), a generalization of the Longest Common Subsequence problem, where the input sequences are over the union of two disjoint sets of symbols, a set of mandatory symbols and a set of optional symbols. We show that different versions of the problem are APX-hard even for instances with two sequences. Moreover, we show that the related problem of determining the existence of a feasible solution of the Exemplar Longest Common Subsequence of two sequences is NP-hard. On the positive side, we first present an efficient algorithm for the ELCS problem over instances of two sequences where each mandatory symbol can appear in total at most three times in the sequences. Furthermore, we present two fixed parameter algorithms for the ELCS problem over instances of two sequences where the parameter is the number of mandatory symbols. |
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| 1: | Dipartimento di Informatica Sistemistica e Comunicazione (DISCo) |
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UNIVERSITÀ DEGLI STUDI DI MILANO-BICOCCA |
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| 2: | Dipartimento di Statistica |
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UNIVERSITÀ DEGLI STUDI DI MILANO-BICOCCA |
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| 3: | Dipartimento di Scienze dei Linguaggi, della Comunicazione e degli Studi Culturali |
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Università degli studi di Bergamo |
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| 4: | 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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| 5: | Laboratoire d'Informatique Gaspard-Monge (LIGM) |
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Université Paris-Est Marne-la-Vallée (UPEMLV) – ESIEE – Ecole des Ponts ParisTech – Fédération de Recherche Bézout – CNRS : UMR8049 |
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| Algorithmics |
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| Subject | : | Computer Science/Bioinformatics Life Sciences/Quantitative Methods Computer Science/Data Structures and Algorithms Computer Science/Computational Complexity |
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| Longest common subsequence – comparative genomics – algorithm design and analysis – combinatorial algorithms – analysis of algorithms and problem complexity. |
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| Attached file list to this document: | |||||
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| hal-00417728, version 1 | |
| http://hal.archives-ouvertes.fr/hal-00417728 | |
| oai:hal.archives-ouvertes.fr:hal-00417728 | |
| From: Guillaume Fertin | |
| Submitted on: Wednesday, 16 September 2009 16:48:07 | |
| Updated on: Wednesday, 16 September 2009 16:50:37 | |
