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DeepCRISPR: optimized CRISPR guide RNA design by deep learning

by Zhou, Chi , Ma, Hanhui , Huang, Deshuang , Chen, Ke , Chuai, Guohui , Liu, Qi , Chen, Ming , Duan, Bin , Qu, Sheng , Wei, Jia , Zhu, Chenyu , Yan, Jifang , Gu, Feng , Xue, Dongyu , Hong, Nanfang

in Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Cell Line / Cell Line, Tumor / Clustered Regularly Interspaced Short Palindromic Repeats - genetics / Computational Biology - methods / Computer applications / Computer Simulation / CRISPR / CRISPR system / CRISPR-Cas Systems - genetics / Data processing / Deep learning / Deoxyribonucleic acid / Design / DNA / Epigenetics / Evolutionary Biology / Gene knockout / genome / Genomes / HCT116 Cells / HEK293 Cells / HeLa Cells / HL-60 Cells / Human Genetics / Humans / Hypotheses / Learning algorithms / Life Sciences / Machine Learning / Method / Microbial Genetics and Genomics / Off-targets / On-targets / Plant Genetics and Genomics / prediction / Ribonucleic acid / RNA / RNA Editing - genetics / RNA, Guide, CRISPR-Cas Systems - genetics / Target recognition

2018

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DeepCRISPR: optimized CRISPR guide RNA design by deep learning

by Zhou, Chi , Ma, Hanhui , Huang, Deshuang , Chen, Ke , Chuai, Guohui , Liu, Qi , Chen, Ming , Duan, Bin , Qu, Sheng , Wei, Jia , Zhu, Chenyu , Yan, Jifang , Gu, Feng , Xue, Dongyu , Hong, Nanfang

2018

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DeepCRISPR: optimized CRISPR guide RNA design by deep learning

by Zhou, Chi , Ma, Hanhui , Huang, Deshuang , Chen, Ke , Chuai, Guohui , Liu, Qi , Chen, Ming , Duan, Bin , Qu, Sheng , Wei, Jia , Zhu, Chenyu , Yan, Jifang , Gu, Feng , Xue, Dongyu , Hong, Nanfang

2018

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Journal Article

DeepCRISPR: optimized CRISPR guide RNA design by deep learning

Zhou, Chi,

Ma, Hanhui,

Huang, Deshuang,

Chen, Ke,

Chuai, Guohui,

Liu, Qi,

Chen, Ming,

Duan, Bin,

Qu, Sheng,

Wei, Jia,

Zhu, Chenyu,

Yan, Jifang,

Gu, Feng,

Xue, Dongyu,

Hong, Nanfang

2018

Overview

A major challenge for effective application of CRISPR systems is to accurately predict the single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would facilitate the optimized design of sgRNAs with high sensitivity and specificity. Here we present DeepCRISPR , a comprehensive computational platform to unify sgRNA on-target and off-target site prediction into one framework with deep learning, surpassing available state-of-the-art in silico tools. In addition, DeepCRISPR fully automates the identification of sequence and epigenetic features that may affect sgRNA knockout efficacy in a data-driven manner. DeepCRISPR is available at http://www.deepcrispr.net/ .

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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Animal Genetics and Genomics

/ Bioinformatics

/ Biomedical and Life Sciences

/ Cell Line

/ Cell Line, Tumor

/ Clustered Regularly Interspaced Short Palindromic Repeats - genetics

/ Computational Biology - methods