Seeker: alignment-free identification of bacteriophage genomes by deep learning
Seeker: alignment-free identification of bacteriophage genomes by deep learning
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DOI：
10.1093/nar/gkaa856
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发表时间：
2020-12-02
影响因子：
14.9
通讯作者：
Koonin, Eugene, V
中科院分区：
文献类型：
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作者：
Auslander, Noam;Gussow, Ayal B.;Koonin, Eugene, V
宏基因组测序的最新进展使得能够发现不同的、独特的微生物和病毒。噬菌体是地球上最丰富的生物实体，进化迅速，因此，在序列数据集中检测未知噬菌体是一个挑战。大多数现有的检测方法依赖于与已知噬菌体序列的序列相似性，阻碍了不同的、高度不同的噬菌体家族的鉴定和表征。在这里，我们介绍了Seeker，这是一种用于无干扰识别噬菌体序列的深度学习工具。Seeker允许快速检测噬菌体蛋白序列数据集并区分噬菌体序列和细菌序列。即使这些噬菌体与已建立的噬菌体家族显示出很小的序列相似性。我们全面验证搜索者的能力，以确定以前未识别的噬菌体，并采用这种方法来检测未知的噬菌体，其中一些是高度不同的已知的噬菌体家族。我们提供了一个门户网站（seeker.pythonanywhere.com）和一个用户友好的Python包（github.com/gussow/seeker），使研究人员能够轻松地将Seeker应用于宏基因组研究，用于检测各种未知的噬菌体。
Recent advances in metagenomic sequencing have enabled discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequence datasets is a challenge. Most of the existing detection methods rely on sequence similarity to known bacteriophage sequences, impeding the identification and characterization of distinct, highly divergent bacteriophage families. Here we present Seeker, a deep-learning tool for alignment-free identification of phage sequences. Seeker allows rapid detection of phages in sequence datasets and differentiation of phage sequences from bacterial ones. even when those phages exhibit little sequence similarity to established phage families. We comprehensively validate Seeker's ability to identify previously unidentified phages, and employ this method to detect unknown phages, some of which are highly divergent from the known phage families. We provide a web portal (seeker.pythonanywhere.com ) and a user-friendly Python package (github.com/gussow/ seeker) allowing researchers to easily apply Seeker in metagenomic studies, for the detection of diverse unknown bacteriophages.