A complexity and approximation framework for the maximization scaffolding problem
We explore in this paper some complexity issues inspired by the contig scaffolding problem in bioinformatics. We focus on the following problem: given an undirected graph with no loop, and a perfect matching on this graph, find a set of cycles and paths covering every vertex of the graph, with edges...
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| Vydáno v: | Theoretical computer science Ročník 595; s. 92 - 106 |
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| Hlavní autoři: | , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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Elsevier B.V
30.08.2015
Elsevier |
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| ISSN: | 0304-3975, 1879-2294 |
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| Abstract | We explore in this paper some complexity issues inspired by the contig scaffolding problem in bioinformatics. We focus on the following problem: given an undirected graph with no loop, and a perfect matching on this graph, find a set of cycles and paths covering every vertex of the graph, with edges alternatively in the matching and outside the matching, and satisfying a given constraint on the numbers of cycles and paths. We show that this problem is NP-complete, even in planar bipartite graphs. Moreover, we show that there is no subexponential-time algorithm for several related problems unless the Exponential-Time Hypothesis fails. Lastly, we also design two polynomial-time approximation algorithms for complete graphs. |
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| AbstractList | We explore in this paper some complexity issues inspired by the contig scaffolding problem in bioinformatics. We focus on the following problem: given an undirected graph with no loop, and a perfect matching on this graph, find a set of cycles and paths covering every vertex of the graph, with edges alternatively in the matching and outside the matching, and satisfying a given constraint on the numbers of cycles and paths. We show that this problem is NP-complete, even in planar bipartite graphs. Moreover, we show that there is no subexponential-time algorithm for several related problems unless the Exponential-Time Hypothesis fails. Lastly, we also design two polynomial-time approximation algorithms for complete graphs. |
| Author | Chateau, A. Giroudeau, R. |
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| Cites_doi | 10.1002/net.3230200106 10.1093/bioinformatics/btu280 10.1145/1290672.1290685 10.1016/j.disc.2012.10.010 10.1016/S0304-3975(02)00577-7 10.1038/nbt.2727 10.4153/CJM-1954-033-3 10.1186/1471-2105-11-345 10.1006/jcss.2000.1727 10.1145/321941.321942 10.1093/bioinformatics/bts175 10.1007/s00224-012-9412-5 10.1089/cmb.2011.0170 10.1006/jcss.2001.1774 10.1093/bioinformatics/bts716 10.1145/585265.585267 |
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| Keywords | Scaffolding Polynomial-time approximation algorithm Complexity |
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| Title | A complexity and approximation framework for the maximization scaffolding problem |
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