The life cycle of temperate phages includes a lysogenic cycle stage when the phage integrates into the host genome and becomes a prophage. However, the identification of prophages that are highly divergent from known phages remains challenging. In this study, by taking advantage of the lysis-lysogeny switch of temperate phages, we designed Prophage Tracer, a tool for recognizing active prophages in prokaryotic genomes using short-read sequencing data, independent of phage gene similarity searching. Prophage Tracer uses the criterion of overlapping split-read alignment to recognize discriminative reads that contain bacterial (attB) and phage (attP) att sites representing prophage excision signals. Performance testing showed that Prophage Tracer could predict known prophages with precise boundaries, as well as novel prophages. Two novel prophages, dsDNA and ssDNA, encoding highly divergent major capsid proteins, were identified in coral-associated bacteria. Prophage Tracer is a reliable data mining tool for the identification of novel temperate phages and mobile genetic elements. The code for the Prophage Tracer is publicly available at https://github.com/WangLab-SCSIO/Prophage_Tracer.

中文翻译：

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Prophage Tracer：使用重叠拆分读取对齐精确追踪原核基因组中的前噬菌体

温带噬菌体的生命周期包括溶原性循环阶段，此时噬菌体整合到宿主基因组中并成为原噬菌体。然而，与已知噬菌体高度不同的前噬菌体的鉴定仍然具有挑战性。在这项研究中，通过利用温带噬菌体的裂解-溶原性转换，我们设计了 Prophage Tracer，这是一种使用短读长测序数据识别原核基因组中活性原噬菌体的工具，独立于噬菌体基因相似性搜索。Prophage Tracer 使用重叠拆分读取对齐的标准来识别包含代表前噬菌体切除信号的细菌 (attB) 和噬菌体 (attP) att 位点的判别性读取。性能测试表明，Prophage Tracer 可以预测具有精确边界的已知前噬菌体，以及新的前噬菌体。两个新的预言，在珊瑚相关细菌中鉴定出编码高度不同的主要衣壳蛋白的 dsDNA 和 ssDNA。Prophage Tracer 是一种可靠的数据挖掘工具，用于鉴定新型温带噬菌体和移动遗传元件。Prophage Tracer 的代码可在 https://github.com/WangLab-SCSIO/Prophage_Tracer 公开获得。