Abstract
We describe in this paper an approximation algorithm for the scaffolding problem, which is part of genome inference in bioinformatics. The aim of the problem is to find a maximum weighted collection of disjoint alternating cycles and paths covering a particular graph called scaffold graph. The problem is known to be NP-complete, and we describe further result concerning a special class of graphs aiming to be close to real instances. The described algorithm is the first polynomial-time approximation algorithm designed for this problem on non-complete graphs.
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Notes
- 1.
We use here “alternating” in an abusive manner, meaning alternating matching edges and non-matching edges, beginning and ending with non-matching edges.
References
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A Appendix
A Appendix
1.1 A.1 Algorithms
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Davot, T., Chateau, A., Giroudeau, R., Weller, M. (2019). New Polynomial-Time Algorithm Around the Scaffolding Problem. In: Holmes, I., Martín-Vide, C., Vega-Rodríguez, M. (eds) Algorithms for Computational Biology. AlCoB 2019. Lecture Notes in Computer Science(), vol 11488. Springer, Cham. https://doi.org/10.1007/978-3-030-18174-1_2
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