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CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes.
Lei Sun1,2,3,4, Jinbiao Wang5,6, Fu Yan5,6
1School of Information Engineering, Yangzhou University, Yangzhou, People's Republic of China. sunlei@yzu.edu.cn.
BMC Bioinformatics
|May 24, 2022
Summary
CrisprVi is a new Python tool that visually analyzes clustered regularly interspaced short palindromic repeats (CRISPR) and their spacers in prokaryotic genomes. It offers enhanced interactivity for researchers studying CRISPR-Cas systems.
Area of Science:
- Bioinformatics
- Genomics
- Microbiology
Background:
- Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated spacers are key elements of prokaryotic CRISPR-Cas systems.
- Analyzing CRISPR loci across multiple genomes requires intuitive and comparative visualization methods.
Purpose of the Study:
- To introduce CrisprVi, a novel visualization analysis tool designed for CRISPR loci.
- To provide researchers with an intuitive and comparative method for analyzing CRISPR sequences in prokaryotic genomes.
Main Methods:
- Development of CrisprVi as a Python package with a graphical user interface (GUI).
- Integration of command parsing, data transmission, local SQLite and BLAST databases, and a data processing function layer.
- Implementation of interactive visualization for CRISPR direct repeats (DRs) and spacers, including display, labeling, and alignment.
Main Results:
- CrisprVi visually presents CRISPR DRs and spacers, detailing their genomic order, IDs, and coordinates.
- The tool offers enhanced interactivity compared to existing tools like CRISPRviz and CRISPRStudio.
- Basic statistics and consensus sequences of DRs/spacers are provided via a clustering heatmap based on BLAST results.
Conclusions:
- CrisprVi serves as a convenient and effective tool for visualizing and analyzing CRISPR sequences.
- The tool aids researchers in inspecting novel CRISPR-Cas systems in prokaryotes.
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