Exploring Frequented Regions in Pan-Genomic Graphs
Exploring Frequented Regions in Pan-Genomic Graphs
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DOI：
10.1109/tcbb.2018.2864564
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发表时间：
2019-09-01
影响因子：
4.5
通讯作者：
Mumey, Brendan
中科院分区：
文献类型：
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作者：
Cleary, Alan;Ramaraj, Thiruvarangan;Mumey, Brendan
我们考虑的问题，确定区域内的泛基因组德布鲁因图，许多序列路径遍历。我们定义这样的区域和子路径，遍历它们的频繁区域（FR）。在这项工作中，我们正式的FR问题，并描述了一个有效的算法，寻找FR。随后，我们提出了一些基于机器学习和泛基因组图简化的FR的应用。我们证明了这些应用程序的有效性，使用数据集的生物体金黄色葡萄球菌（细菌）和酿酒酵母（酵母）。我们证实了FR的生物相关性，如识别酵母中的基因渗入，有助于酒精耐受性，并表明FR可用于工业用途和可视化泛基因组空间的酵母菌株分类。
We consider the problem of identifying regions within a pan-genome De Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In this work, we formalize the FR problem and describe an efficient algorithm for finding FRs. Subsequently, we propose some applications of FRs based on machine-learning and pan-genome graph simplification. We demonstrate the effectiveness of these applications using data sets for the organisms Staphylococcus aureus (bacterium) and Saccharomyces cerevisiae (yeast). We corroborate the biological relevance of FRs such as identifying introgressions in yeast that aid in alcohol tolerance, and show that FRs are useful for classification of yeast strains by industrial use and visualizing pan-genomic space.