Scaffolding Algorithms

Mandric, Igor; Lindsay, James; Măndoiu, Ion; Zelikovsky, Alexander

doi:10.1002/9781119272182.ch5

Cited by 7 publications

(7 citation statements)

References 24 publications

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“…The mathematical problem modeling this inference, called Scaffolding, is made complicated by possible inconsistencies in the pairing information. See [3] for a recent overview of models, variants, and methods in this context.…”

Section: Introductionmentioning

confidence: 99%

On a Greedy Approach for Genome Scaffolding

Davot¹,

Château²,

Fossé³

et al. 2021

Preprint

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Background: Scaffolding is a bioinformatics problem aimed at completing the contig assembly process by determining the relative position and orientation of these contigs. It can be seen as a paths and cycles cover problem of a particular graph called the “scaffold graph”.Results: We provide some NP-hardness and inapproximability results on this problem. We also adapt a greedy approximation algorithm on complete graphs so that it works on a special class 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.Conclusion: Tests on a set of simulated instances show that our algorithm provides better results than the version on complete graphs.

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Section: Introductionmentioning

confidence: 99%

On a Greedy Approach for Genome Scaffolding

Davot¹,

Château²,

Fossé³

et al. 2021

Preprint

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“…Previous work focuses on the production of sequences by solving the so-called Scaffolding problem in this graph [4,14,16]. Scaffolding is a widely studied problem in bioinformatics and can be modeled by numerous, mostly heuristic, methods [8].…”

Section: Introductionmentioning

confidence: 99%

Linearizing Genomes: Exact Methods and Local Search

Davot

Château

Giroudeau

et al. 2020

SOFSEM 2020: Theory and Practice of Computer Science

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In this article, we address the problem of genome linearization from the perspective of Polynomial Local Search, a complexity class related to finding local optima. We prove that the linearization problem, with a neighborhood structure, the neighbor slide, is PLS-complete. On the positive side, we develop two exact methods, one using tree decompositions with an efficient dynamic programming, the other using an integer linear programming. Finally, we compare them on real instances. a b c d e f g h AT CT T m = 1 CCT m = 2 T AA m = 1 CAT G m = 1 26 7 9 3 1 1 2

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“…Formally, it is possible to extract from this information a set of relationships between the contigs, that may be inconsistent. A survey on recent methods is available in [5]. The problem that we model here is more general than those presented in the literature, and therefore allows adaptation towards realistic modelization.…”

Section: Introductionmentioning

confidence: 99%

New Polynomial-Time Algorithm Around the Scaffolding Problem

Davot

Château

Giroudeau

et al. 2019

Algorithms for Computational Biology

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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 polynomialtime approximation algorithm designed for this problem on non-complete graphs.

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Scaffolding Algorithms

Cited by 7 publications

References 24 publications

On a Greedy Approach for Genome Scaffolding

On a Greedy Approach for Genome Scaffolding

Linearizing Genomes: Exact Methods and Local Search

New Polynomial-Time Algorithm Around the Scaffolding Problem

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