Horizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in antibiotic resistance or the outbreak of virulent strains. Detection of HGT and the mechanisms responsible and enabling it, is hence of prime importance.Existing algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from its recipient genome. Closely related species pose an even greater challenge as most genes are very similar and therefore, the phylogenetic signal is weak anyhow. Notwithstanding, the importance of detecting HGT between such organisms is extremely high for the role of HGT in the emergence of new highly virulent strains. In a recent work we devised a novel technique that relies on loss of synteny around a gene as a witness for HGT. We used a novel heuristic for synteny measurement, SI (Syntent Index), and the technique was tested on both simulated and real data and was found to provide a greater sensitivity than other HGT techniques. This synteny–based approach suffers low specificity, in particular more closely related species. Here we devise an adaptive approach to cope with this by varying the criteria according to species distance. The new approach is doubly adaptive as it also considers the lengths of the genes being transferred. In particular, we use Chernoff bound to decree HGT both in simulations and real bacterial genomes taken from EggNog database. Here we show empirically that this approach is more conservative than the previous χ2 based approach and provides a lower false positive rate, especially for closely related species and under wide range of genome parameters.

中文翻译：

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检测水平基因转移：一种概率方法

水平基因转移（HGT）是DNA序列在物种之间转移而不是通过遗传的事件。HGT是原核生物进化的关键因素，并且是导致抗生素耐药性或强毒株爆发的基因组新颖性的重要来源。因此，对HGT及其负责机制的检测至关重要。现有算法依靠强大的系统发育信号将转移的序列与其受体基因组区分开。密切相关的物种面临更大的挑战，因为大多数基因非常相似，因此无论如何系统发生信号都很弱。尽管如此，对于在新的高毒力菌株中HGT的作用，检测这些生物之间的HGT的重要性非常高。在最近的工作中，我们设计了一种新技术，该技术依赖于基因周围的同义性丧失作为HGT的见证。我们使用了一种新颖的试探法来进行语气测量，SI（语气指数），并且对该技术进行了模拟和真实数据测试，结果发现它比其他HGT技术具有更高的灵敏度。这种基于同义关系的方法特异性低，特别是与物种密切相关的物种。在这里，我们设计了一种自适应方法来解决此问题，方法是根据物种距离改变标准。这种新方法具有双重适应性，因为它也考虑了被转移基因的长度。特别是，我们在仿真和从EggNog数据库获取的真实细菌基因组中都使用Chernoff绑定法来命令HGT。