Dynamique des Structures et Interactions des Macromolécules Biologiques, Institut National de la Santé et de la Recherche Médicale UMR-S 665, Université Paris Diderot, Institut National de la Transfusion Sanguine, Paris, France.
PLoS One. 2010 Apr 1;5(4):e9989. doi: 10.1371/journal.pone.0009989.
Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity.
水平基因转移 (HGT) 似乎对原核生物的物种进化具有重要意义。因此，已经设计了许多仅使用基因组中嵌入的信息的参数方法来检测 HGT。许多报告指出，将相同的基因组应用于不同方法的结果存在不一致性。使用所有 HGT 参数都受到控制的人工基因组可以在相同条件下测试不同的方法。这项针对 16 种代表性参数方法的基准测试的结果显示出效率的多样性。有些方法无论 HGT 类型如何都效果很差，有些方法则取决于条件或使用的指标。在总误差方面表现最好的方法是那些使用四核苷酸作为窗口方法的标准的方法，或者那些使用密码子使用频率作为基于基因的方法和柯尔莫哥洛夫-莱布勒散度度量的方法。窗口方法非常敏感但特异性较低，并且难以检测孤立的单个基因。另一方面，基于基因的方法通常特异性很高但缺乏敏感性。我们建议将两种方法结合使用，以充分发挥每种类别的优势，一种是基于基因的特异性方法，另一种是基于窗口的敏感性方法。
