Choosing a Target Sequence for Gene Editing – on sgRNA design

Michał Chromiak, Michał Lupa

Abstract


The CRISPR-Cas9 system is being widely used for genome engineering in many different biological applications. As a prokaryotic adaptive immunity system, that was originally adapted from the bacterial Type II CRISPR, CRISPR-Cas9 uses a non-coding RNAs. Those RNAs guides Cas9 nuclease, which in turn induce site-specific DNA cleavage at a specific locations in genome. Such mechanism gives an opportunity to create a programmable method for genome editing. The first step in a CRISPR/Cas9 gene engineering experiment is to design a custom single guide RNA (sgRNA). This paper discusses a possible way of organizing data for designing sgRNA using a fast and general-purpose cluster computing system based on MapReduce paradigm.

Keywords


crispr; gene editing; mapreduce; gRNA; sgRNA; PAM

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References


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DOI: http://dx.doi.org/10.21936/si2017_v38.n2.798