A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.
A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.
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DOI：
10.1038/srep30308
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发表时间：
2016-07-25
影响因子：
4.6
通讯作者：
Ragan MA
中科院分区：
文献类型：
--
作者：
Cong Y;Chan YB;Ragan MA
侧向遗传转移(LGT)在微生物进化中起着重要作用。现有的用于检测假定的侧向起源的基因组区域的计算方法在大数据范围内的规模很小。这里，我们提出了一种新的方法，该方法基于TF-IDF(术语频率-反向文档频率)统计量，不仅可以在层次结构的核苷酸或蛋白质序列集中检测侧向起源区域，而且还可以检测它们的起源和转移方向。该方法基于序列中k-MERS的频率分布。如果一组相邻的k-mers在另一个系统群中出现的频率比在它自己的系统群中出现的频率高，我们可以推断它们已经从第一个系统群转移到了第二个系统群。我们使用模拟数据集和经验数据集对TF-IDF进行了严格的测试。利用模拟数据，我们在不同的参数设置下测试了我们的方法，包括序列长度、组内和组内替换率以及LGT后的替换率、删除率、转移区域长度和k大小，发现我们的方法能够以较高的准确率和召回率检测LGT事件。我们的方法比已有的ALFY方法性能更好，后者召回率高但准确率低。我们的方法是有效的，运行时间随着序列长度的增加而近似线性增加。
Lateral genetic transfer (LGT) plays an important role in the evolution of microbes. Existing computational methods for detecting genomic regions of putative lateral origin scale poorly to large data. Here, we propose a novel method based on TF-IDF (Term Frequency-Inverse Document Frequency) statistics to detect not only regions of lateral origin, but also their origin and direction of transfer, in sets of hierarchically structured nucleotide or protein sequences. This approach is based on the frequency distributions of k-mers in the sequences. If a set of contiguous k-mers appears sufficiently more frequently in another phyletic group than in its own, we infer that they have been transferred from the first group to the second. We performed rigorous tests of TF-IDF using simulated and empirical datasets. With the simulated data, we tested our method under different parameter settings for sequence length, substitution rate between and within groups and post-LGT, deletion rate, length of transferred region and k size, and found that we can detect LGT events with high precision and recall. Our method performs better than an established method, ALFY, which has high recall but low precision. Our method is efficient, with runtime increasing approximately linearly with sequence length.