Detection method for functional prophage as well as location and sequence thereof in bacteria

Abstract

The invention discloses a detection method for functional prophage as well as location and sequence thereof in bacteria. The detection method in the invention includes steps of: predicting an openingreading frame in the genome sequencing data of to-be-detected bacteria to obtain the proteins encoded by the opening reading frame, and comparing the protein sequence with the sequences in the proteinlibrary of the phage, wherein the proteins which are matched with the phage proteins are the functional proteins; searching a positive repeating sequence on the encoding genes of the functional proteins as well as upstream and downstream thereof, wherein a sequence between two positive repeating sequences is the candidate sequence of a candidate prophage; connecting the head and the tail of the candidate sequence, wherein the candidate prophage containing the sequencing read length crossing the head-to-tail connection of the candidate sequence is the functional phage, whereas the candidate prophage without the sequencing read length crossing the head-to-tail connection of the candidate sequence is not the functional phage. The method is simple in operation and has great application prospect.

Description

technical field [0001] The invention relates to a method for detecting functional prophage in bacteria and its position and sequence in the field of biotechnology. Background technique [0002] A phage is a virus that infects bacteria and plays important biological roles in the host. They can be divided into two classes: lytic and lysogenic phages. Lysogenic phage is a virus that can integrate its own gene into the bacterial genome. During the integration process, lysogenic phage can insert its gene into the bacterial genome (the integration of lysogenic phage into the bacterial genome is called pre phage) or in the cytoplasm of bacteria in the form of plasmids. [0003] As an important form of phage, prophage plays an important role in the evolution of prokaryotes and is also the driving force of bacterial genome diversification. During the integration of prophage into bacteria, it can change the gene expression of the host and destroy the bacterial original genome, and ...

AI Technical Summary

Problems solved by technology

However, through the verification of biological experiments, it was found that many prophages predicted by these tools could not be induced; and some functional prophages that could be induced were quite different from the previous prediction results, there was a deviation in the predicted position, and the functional prophage could not be accurately predicted Case

Therefore, none of these tools can predict the precise location of a functional prophage

Also, they cannot automatically extract complete functional prophage genome sequences from bacterial genomes

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