crisprTool.md

CRISPR Online Tool for Cas9 and Cas12 Efficacy Prediction

Description

The CRISPRtool is a deep learning-based adaptive ensemble method, integrating context-based sequence features with specific cell line characteristics to enhance the design of on-target sgRNAs within CRISPR/Cas9 and Cas12 systems. CRISPRtool integrates six parallel deep learning-based models, including two previously proposed models (DeepCRISPR and Seq-deepCpf1) and four our customized models, Cas9/Cas12_SimpleRNN, Cas9/Cas12_BiLSTM, Cas9/Cas12_Attention, and Cas9/Cas12_Transformer. For more details, please refer to Qingyang Liu, Wentian Wang, Shangjia Li, et al. CRISPRtool: Adaptive Deep Learning for Optimal CRISPR sgRNA Prediction across Cas9 and Cas12 Systems. 2026.

Here, we provide a free wet-lab-friendly website that incorporates our powerful predictors for personalized design of on-target sgRNAs for arbitrary gene in CRISPR/Cas9 and Cas12.

Usage

Users can select the system types of CRISPR (Cas9 or Cas12) that they are interested in. Then, if users select 'Normal' mode, which means CRISPRtool will only design sgRNAs based on reference sequences from Ensembl database; you can also select 'Mutation related to MDA-MB-231' mode if you are interested in designing with MDA-MB-231 cell line related mutations. After mode selection, you can specify the gene you want to design. Finally, click the 'Go Cas9/Cas12 on-target prediction' button, you will get design results for specific gene after several minutes!

The output of design results includes the table showing all candidate sgRNAs for one gene, and users can choose to download them by clicking 'Download GenBank and CSV files as ZIP' button. Note that for 'Mutation related to MDA-MB-231' mode, the last column indicates whether there are any mutations in the target sequence.

Note

You are using version 1.0 of this tool. Once you click the download button, the page will automatically refresh.