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bioRxiv · 10.1101/655779

CRISPRpred(SEQ): a sequence based tool for sgRNA on target activity prediction

Rafid, H.·Toufikuzzaman, M.·Rahman, M. S.
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Abstract

An accurate and fast genome editing tool can be used to treat genetic diseases, modify crops genetically etc. However, a tool that has low accuracy can be risky to use, as incorrect genome editing may have severe consequences. Although many tools have been developed in the past, there are still room for further improvement. In this paper, we present CRISPRpred(SEQ), a sequence based tool for sgRNA on target activity prediction that leverages only traditional machine learning techniques. We compare the results of CRISPRpred(SEQ) with that of DeepCRISPR, the current state-of-the-art, which uses a deep learning pipeline. In spite of using only traditional machine learning methods, we are able to beat DeepCRISPR for the three out of four cell lines in the benchmark dataset convincingly (2.174%, 6.905% and 8.119% improvement for the three cell lines), which is quite outstanding.

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Rafid, H., Toufikuzzaman, M., Rahman, M. S.. 2019-05-30. CRISPRpred(SEQ): a sequence based tool for sgRNA on target activity prediction. https://doi.org/10.1101/655779

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