A research team from the Chinese Academy of Sciences (CAS) has created an interactive web server called CRISPRimmunity, which is an analysis service platform for identifying significant molecular events related to CRISPR and genome editing regulation. The study has been published in Nucleic Acids Research.
The CRISPRimmunity platform is designed for integrated analysis and prediction of CRISPR-Cas and anti-CRISPR systems. It includes customized databases with annotations for known anti-CRISPR proteins, anti-CRISPR-associated proteins, class II CRISPR-Cas systems, CRISPR array types, HTH structural domains, and mobile genetic elements. These resources enable the study of molecular events in the co-evolution of CRISPR-Cas and anti-CRISPR systems.
To enhance prediction accuracy, the researchers utilized homology analysis, association analysis, and self-targeting in prophage regions to predict anti-CRISPR proteins. When tested on data from 99 experimentally validated Acrs and 676 non-Acrs, CRISPRimmunity achieved a 99.7% accuracy for anti-CRISPR protein prediction.
In addition, the platform introduced the first ab initio prediction algorithm for class II CRISPR-Cas systems, revealing several previously unknown proteins. These include four Cas9s with different PAM structural domains, a smaller Cpf1, 61 C2c10s, and three unclassified novel V-type Cas proteins. Some of these proteins have already been experimentally validated for in vitro activity.
CRISPRimmunity offers several advantages. It is an easy-to-use web server that provides a comprehensive analysis platform for CRISPR-related research. It accurately predicts anti-CRISPR proteins and identifies novel class II CRISPR-Cas loci, offering an evolutionary perspective of the CRISPR-Cas and anti-CRISPR systems. Unlike other resources focused on specific domains, CRISPRimmunity fills the gap by providing methods for identifying novel class II CRISPR-Cas systems.
The user-friendly interface offers various visualization and customization options, with machine-readable results and tutorials suitable for users of all levels. The NCBI database grants access to annotated data on 18,408 fully sequenced and 235 Acr-containing bacteria, as well as 208,209 human gut microorganisms, providing information on key CRISPR-associated molecular events.
Users can download or view this data to aid future experimental design and data analysis. Additionally, computational biologists can access a stand-alone version of CRISPRimmunity on Github for bulk data mining.
More information:
Fengxia Zhou et al, CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing, Nucleic Acids Research (2023). DOI: 10.1093/nar/gkad425
Platform: www.microbiome-bigdata.com/CRISPRimmunity/index/
Source code for batch analysis: github.com/HIT-ImmunologyLab/CRISPRimmunity
Citation:
Team develops CRISPR tool with big data visualization platform for genome editing and modification (2023, June 19)
retrieved 19 June 2023
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Shambhu Kumar is a science communicator, making complex scientific topics accessible to all. His articles explore breakthroughs in various scientific disciplines, from space exploration to cutting-edge research.
