CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci
CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci
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DOI：
10.1089/crispr.2020.0059
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发表时间：
2020-12-04
期刊：
影响因子：
3.7
通讯作者：
Sorensen, Soren J.
中科院分区：
文献类型：
--
作者：
Russel, Jakob;Pinilla-Redondo, Rafael;Sorensen, Soren J.
CRISPR-Cas系统的动态特性和不断扩展的分类对其自动分类提出了挑战。在这里，我们开发了CRISPRCasTyper，这是一种基于最新命名法（44个亚型/变体）的自动化工具，具有改进的识别和分型CRISPR阵列和cas位点的能力。作为一项新功能，CRISPRCasTyper使用机器学习方法基于重复序列对CRISPR阵列进行亚型分型，从而允许对孤儿和远端阵列进行分型。CRISPRCasTyper提供了一个图形输出，其中crispr和cas操作子被可视化为基因图谱，从而通过合成帮助部分和新系统的注释。CRISPRCasTyper以一组人工筛选的31种亚型为基准，中位准确率为98.6%，并用于探索150 000个宏基因组中的CRISPR-Cas多样性。总之，我们提出了一种最新的软件，用于改进CRISPR-Cas位点的自动预测。crisprcasyper可以通过conda和web服务器（cctype .crispr）获得。dk)。
Automated classification of CRISPR-Cas systems has been challenged by their dynamic nature and expanding classification. Here, we developed CRISPRCasTyper, an automated tool with improved capabilities for identifying and typing CRISPR arrays and cas loci based on the latest nomenclature (44 subtypes/variants). As a novel feature, CRISPRCasTyper uses a machine learning approach to subtype CRISPR arrays based on the sequences of the repeats, which allows the typing of orphan and distant arrays. CRISPRCasTyper provides a graphical output, where CRISPRs and cas operons are visualized as gene maps, thus aiding annotation of partial and novel systems through synteny. CRISPRCasTyper was benchmarked against a manually curated set of 31 subtypes with a median accuracy of 98.6% and used to explore CRISPR-Cas diversity across >3,000 metagenomes. Altogether, we present an up-to-date software for improved automated prediction of CRISPR-Cas loci. CRISPRCasTyper is available through conda and as a web server (cctyper.crispr.dk ).