细胞质不相容定量锁/键模型的算法。

IF 1.5 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS
Algorithms for Molecular Biology Pub Date : 2020-07-22 eCollection Date: 2020-01-01 DOI:10.1186/s13015-020-00174-1
Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri
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引用次数: 1

摘要

细胞质不相容性(cytoplasimincompatibility, CI)与沃尔巴克氏体对宿主生殖的操纵有关。尽管其广泛发生,但CI的分子基础尚不清楚,并提出了理论模型来理解这一现象。我们在本文中考虑定量的锁-键模型,它目前代表了一个很好的假设,与现有的数据一致。在这种情况下,CI被建模为用最小数量的链子图覆盖二部图的边的问题。这个问题已经被认为是np困难的,我们提供了一个具有非平凡复杂性的指数算法。通常,根据数据集的不同,可能存在许多最优解决方案,这些解决方案在生物学上可能存在很大差异。因此,依赖单一的最优解可能是有问题的。为此,我们讨论了二部图的所有最小链子图覆盖的枚举问题,并证明了该问题可以在拟多项式时间内解决。有趣的是,为了解决上述问题,我们还考虑了二部图的所有极大链子图的枚举问题,并对后者的现有文献结果进行了改进。最后,为了演示我们方法的有效性,我们展示了一个真实数据集上的应用程序。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility.

Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility.

Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility.

Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility.

Cytoplasmic incompatibility (CI) relates to the manipulation by the parasite Wolbachia of its host reproduction. Despite its widespread occurrence, the molecular basis of CI remains unclear and theoretical models have been proposed to understand the phenomenon. We consider in this paper the quantitative Lock-Key model which currently represents a good hypothesis that is consistent with the data available. CI is in this case modelled as the problem of covering the edges of a bipartite graph with the minimum number of chain subgraphs. This problem is already known to be NP-hard, and we provide an exponential algorithm with a non trivial complexity. It is frequent that depending on the dataset, there may be many optimal solutions which can be biologically quite different among them. To rely on a single optimal solution may therefore be problematic. To this purpose, we address the problem of enumerating (listing) all minimal chain subgraph covers of a bipartite graph and show that it can be solved in quasi-polynomial time. Interestingly, in order to solve the above problems, we considered also the problem of enumerating all the maximal chain subgraphs of a bipartite graph and improved on the current results in the literature for the latter. Finally, to demonstrate the usefulness of our methods we show an application on a real dataset.

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来源期刊
Algorithms for Molecular Biology
Algorithms for Molecular Biology 生物-生化研究方法
CiteScore
2.40
自引率
10.00%
发文量
16
审稿时长
>12 weeks
期刊介绍: Algorithms for Molecular Biology publishes articles on novel algorithms for biological sequence and structure analysis, phylogeny reconstruction, and combinatorial algorithms and machine learning. Areas of interest include but are not limited to: algorithms for RNA and protein structure analysis, gene prediction and genome analysis, comparative sequence analysis and alignment, phylogeny, gene expression, machine learning, and combinatorial algorithms. Where appropriate, manuscripts should describe applications to real-world data. However, pure algorithm papers are also welcome if future applications to biological data are to be expected, or if they address complexity or approximation issues of novel computational problems in molecular biology. Articles about novel software tools will be considered for publication if they contain some algorithmically interesting aspects.
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