期刊
SCIENTIFIC REPORTS
卷 6, 期 -, 页码 -出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/srep30870
关键词
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资金
- Department of Biotechnology, Government of India [GAP0001]
- Council of Scientific and Industrial Research, India [BSC0121]
- CSIR-Institute of Microbial Technology, Chandigarh, India
Genome editing by sgRNA a component of CRISPR/Cas system emerged as a preferred technology for genome editing in recent years. However, activity and stability of sgRNA in genome targeting is greatly influenced by its sequence features. In this endeavor, a few prediction tools have been developed to design effective sgRNAs but these methods have their own limitations. Therefore, we have developed ge-CRISPR using high throughput data for the prediction and analysis of sgRNAs genome editing efficiency. Predictive models were employed using SVM for developing pipeline-1 (classification) and pipeline-2 (regression) using 2090 and 4139 experimentally verified sgRNAs respectively from Homo sapiens, Mus musculus, Danio rerio and Xenopus tropicalis. During 10-fold cross validation we have achieved accuracy and Matthew's correlation coefficient of 87.70% and 0.75 for pipeline-1 on training dataset (T-1840) while it performed equally well on independent dataset (V-250). In pipeline-2 we attained Pearson correlation coefficient of 0.68 and 0.69 using best models on training (T-3169) and independent dataset (V-520) correspondingly. ge-CRISPR (http://bioinfo.imtech.res.in/manojk/gecrispr/) for a given genomic region will identify potent sgRNAs, their qualitative as well as quantitative efficiencies along with potential off-targets. It will be useful to scientific community engaged in CRISPR research and therapeutics development.
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