You can use the flyCRISPR Optimal Target Finder tool to identify highly specific target sites in the Drosophila genome. Due to the frequency of naturally occurring SNPs between fly strains, it is a good idea to sequence the region you intend to target in the fly strain you plan to inject i...
A customized open-source bioinformatics pipeline, BLENDER (blunt end finder), then identifies off-target sequences genome wide. DISCOVER-seq is capable of finding and measuring off-targets in primary cells and in situ. The two main advantages of DISCOVER-seq are (i) low false-positive rates ...
perl CRISPRCasFinder.pl[options]-in<filename.fasta>-in:输入序列,fasta格式,后缀可以是.fasta、.fna、.mfa、.fa、.txt-out:输出结果路径-keep:保留过程文件,Prodigal/Prokka、CasFinder、rawFASTA、Properties-html:输出HTML网页格式的结果-so:sel392v2.so文件的路径(这个文件干么的我也不知道,在软件包中有提...
他们基于3个不同样品的宏基因组分析,首先使用HMM模型(Hidden Markov Model)在各种样品的组装重叠群中对已知的Cas蛋白进行比对;接下来,使用CRISPRFinder软件识别CRISPR阵列,然后使用了大于800个残基的未鉴定蛋白的条件进行筛选;最后将这些大蛋白作为潜在的2类Cas效应子进一步分析,进而发现了CRISPR-CasX和CRISPR-CasY系统。
7 PcrIIC1 enhances the DNA-binding capability, PAM tolerance and target cleavage efficiency of CbCas9 by interacting with the CTH domain. a, Top, model of in vivo bacterial genome interference assay for CbCas9 and PcrIIC1. Bottom, bacteria genome interference assay revealed by bacterial culture...
CRISPRCasFinder Nucleic Acids Res. 2018 482 CRISPRTarget RNA Biology 2013 231 MacSyFinder PLoS One 2014 161 CRISPI Bioinformatics 2009 149 CRISPRmap Nucleic Acids Res. 2013 134 Crass Nucleic Acids Research 2013 103 CRISPy-web Synthetic and Systems Biotechnology 2016 88 CRISPRCasTyper The CRISPR Jou...
Various sgRNA design rules and tools have been developed for sgRNA on-target identification and efficacy prediction. These methods are categorized into three types: (1) alignment-based, where the sgRNAs are aligned from the given genome purely by locating the PAM (CasFinder[8], etc.); (2) ...
CRISPR target assessment crRNA: CRISPR RNA DHS: DNase I hypersensitivity DSB: Double-stranded break GFP: Green fluorescent protein gRNA : Guide RNA HDR: Homology-directed repair HEK293: Human embryonic kidney 293 cells IDLV: Integrase-deficient lentiviral vectors KI: Knock-in KO: ...
A customized open-source bioinformatics pipeline, BLENDER (blunt end finder), then identifies off-target sequences genome wide. DISCOVER-seq is capable of finding and measuring off-targets in primary cells and in situ. The two main advantages of DISCOVER-seq are (i) low false-positive rates ...
(Supplementary Fig.1b). For CRISPR array identification, 4963 clusters that contain Type II Cas9 proteins were identified by using the CRISPRFinder43. We first identified the potential crRNA sequences for each cluster, and then the tracrRNA was each identified by crRNA sequence alignment. These ...