title: ge-CRISPR - An integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system.
abstract: 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.
authors: Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh-160036, India.
authors: Karambir
authors: K
authors: Kaur
authors: Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh-160036, India.
authors: Amit Kumar
authors: AK
authors: Gupta
authors: Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh-160036, India.
authors: Akanksha
authors: A
authors: Rajput
authors: Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh-160036, India.
authors: Manoj
authors: M
authors: Kumar
mesh_terms: D000818:Animals; D064113:CRISPR-Cas Systems; D019295:Computational Biology / Q000379:methods*; D000072669:Gene Editing; D006801:Humans; D020407:Internet; D051379:Mice; D000094704:RNA, Guide, CRISPR-Cas Systems / Q000235:genetics*; D060388:Support Vector Machine; D014981:Xenopus; D015027:Zebrafish
chemical_list: D000094704:RNA, Guide, CRISPR-Cas Systems