具体而言，CHOOSER成功地识别了3477个潜在的CRISPR-Cas系统，这一发现不仅扩展了已知的II型、V型和VI型系统的数量，还为科研人员提供了更多关于CRISPR-Cas系统的见解。此外，CHOOSER在这些系统中发现了39个此前未被现有基于比对的工具（如CRISPRCasTyper）所识别的Cas12候选者，并进一步鉴定出11个Casλ同源物。这些同源...
Create the environment with CRISPRCasTyper and all dependencies and database conda create -n cctyper -c conda-forge -c bioconda -c russel88 cctyper pip If you have the dependencies (Python >= 3.8, HMMER >= 3.2, Prodigal >= 2.6, minced, grep, sed) in your PATH you can install with ...
CHOOSER在这些系统中发现了39个此前未被现有基于比对的工具(如CRISPRCasTyper)识别的Cas12候选者,并在其中鉴定出11个Casλ同源物,所有这些同源物均被预测为具备自我处理pre-crRNA的功能。实验验证进一步确认了其中一种名为EphcCasλ的Casλ同源物的pre-crRNA处理活性和DNase活性。 图2. EphcCasλ的pre-crRNA处理活性...
CRISPRCasTyper can be installed either through conda or pip. It is advised to use conda, since this installs CRISPRCasTyper and all dependencies, and downloads the database in one go. Conda Useminicondaoranacondato install. Create the environment with CRISPRCasTyper and all dependencies and dat...
主要有两种策略用于识别Cas蛋白:1)基于氨基酸序列相似性的方法,这种方法简单直接,如NCBI的PGAP和CRISPRCasTyper等生物信息学工具,依赖于BLAST比对和已知Cas蛋白的HMM模型搜索。然而,这种方法可能遗漏远缘同源蛋白;2)基于结构相似性的方法,这种策略基于生物学中“结构-功能”关系,即蛋白质的功能由其结构决定。随着蛋白质...
三、 bioRxiv：新的CRISPR loci预测⼯具-CRISPRCasTyper CRISPR-Cas位点编码⾼度多样化的原核⽣物适应性防御系统，最近因其在基因编辑等⽅⾯的应⽤⽽变得流⾏。对于系统检测和分类CRISPR-Cas系统的⽣物信息学⼯具的需求⽇益增长。CRISPRCasTyper使⽤机器学习⽅法根据直接重复序列对CRISPR数组进⾏...
by using MinCED v0.4.2 [15]. They included consensus repeats from all arrays located within 1 kbp of a Cas operon, resulting in a total of 5,838 subtyped repeat sequences. The benchmark dataset can be downloaded from the following linkhttps://github.com/Russel88/CRISPRCasTyper/tree/...
The discovery of CRISPR-Cas systems has paved the way for advanced gene editing tools. However, traditional Cas discovery methods relying on sequence similarity may miss distant homologs and aren’t suitable for functional recognition. With protein large language models (LLMs) evolving, there is pot...
除了CRISPR检测外,van Riet还报告了在336个hCRISPR的侧翼区域中检测到cas基因。 然而,他们的研究中既没有提供序列,也没有提供这些cas基因的显著性值。 但是Blake Wiedenheft等人使用CRISPRCasFinder和CRISPRCasTyper并没能重现人类参考基因组中cas基因。 考虑到 van Riet等人筛选用的人类参考基因组最初是20年前组装的...
Multidrug resistance in Pseudomonas aeruginosa, a high-priority pathogen per the World Health Organization, poses a global threat due to carbapenem resistance and limited antibiotic treatments. Using the bioinformatic tools CRISPRCasFinder, CRISPRCasTyper, CRISPRloci, and CRISPRImmu...