CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
By Yuki Naito, Hidemasa Bono, Kumiko Ui-Tei. Bioinform., 2014
1,145 citations recorded by the source corpus.
Summary: CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided by Cas9 nuclease in complex with a guide RNA (gRNA), that complementarily binds to a ∼20 nt targeted sequence. The target sequence requirements are twofold. First, the 5′-NGG protospacer adjacent motif (PAM) sequence must be located adjacent to the target sequence. Second, the target sequence should be specific within the entire genome in order to avoid off-target editing. CRISPRdirect enables users to easily select rational target sequences with minimized off-target sites by performing exhaustive searches against genomic sequences. The server currently incorporates the genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. Availability: Freely available at http://crispr.dbcls.jp/. Contact: y-naito@dbcls.rois.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Business and International Management, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/e198d1f495b79ba417166acc10f43c8c3f33a190
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In Molecular Biology
Citations in the corpus
- Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites (2015, neutral): “…(Aach et al., 2014; Cradick et al., 2014; Doench et al., 2014; Bae et al., 2014a; Heigwer et al., 2014; Hsu et al., 2013; Lei et al., 2014; Montague et al., 2014; O'Brien and Bailey, 2014; Naito et al., 2014; Sander et al., 2010; Upadhyay and Sharma, 2014; Xie et al., 2014; Zhu et al., 2014).”
- Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR (2016, background): “Although published tools and scoring systems allow ranking sequences by specificity [10–22] and efficiency [2, 8, 23–25], they are usually limited to a handful of genomes and only few evidence-based recommendations exist to optimize offtarget search parameters and on-target efficiency.”