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CRSeek: a Python module for facilitating complicated CRISPR design strategies

PeerJ Preprints. 2018; 
Will Dampier​, , Cheng-Han Chung, Neil T Sullivan, Andrew J Atkins, Michael R Nonnemacher, , Brian Wigdahl​,
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Gene Synthesis The CRISPR-Cas system has revolutionized the gene editing field (Doudna and Charpentier, 2014).40It has democratized the field by lowering the difficulty of editing a specific genomic locus (Genscript,412016). Various applications of CRISPR-Cas systems have been developed with useful properties such42as an inducible expression system (Cao et al., 2016), tissue specificity (Ablain et al., 2015), as well as43advanced editing strategies (Kim et al., 2017). In practice, targeting a specific locus with any of these44systems simply involves finding a protospacer adjacent motif (PAM) next to a unique 20 bp protospacer45and performing basic molecular biology techniques (Genscript, 2016; Sternberg and Doudna, 2015 Get A Quote

摘要

With the popularization of the CRISPR-Cas gene editing system there has been an explosion of new techniques made possible by this versatile technology. However, the computational field has lagged behind with a current lack of computational tools for developing complicated CRISPR-Cas gene editing strategies. We present crseek, a Python package that provides a consistent application programming interface (API) for multiple cleavage prediction algorithms. Four popular cleavage prediction algorithms were implemented and further adapted to work on draft-quality genomes. Furthermore, since crseek mirrors the popular scikit-learn API, the package can be easily integrated as an upstream processing module for facilitati... More

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