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).

中文翻译：

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CRISPRCasTyper：CRISPR-Cas 位点的自动识别、注释和分类


CRISPR-Cas 系统的自动分类因其动态性质和扩展分类而受到挑战。在这里，我们开发了 CRISPRCasTyper，这是一种自动化工具，具有改进的功能，可根据最新的命名法（44 个亚型/变体）识别和分型 CRISPR 阵列和cas位点。作为一项新颖功能，CRISPRCasTyper 使用机器学习方法根据重复序列对 CRISPR 阵列进行亚型分类，从而可以对孤立阵列和远程阵列进行分型。 CRISPRCasTyper 提供图形输出，其中 CRISPR 和cas操纵子可视化为基因图谱，从而通过同线性帮助注释部分和新颖的系统。 CRISPRCasTyper 以手动管理的 31 个亚型集为基准，中位准确度为 98.6%，并用于探索超过 3,000 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。 CRISPRCasTyper 可通过 conda 并作为 Web 服务器 (cctyper.crispr.dk) 获得。