Choosing a Target Sequence for Gene Editing – on sgRNA design

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.