Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment.

ABSTRACT: 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 bou

SUBMITTER: Tang K 

PROVIDER: S-EPMC8682789 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature