PUBLICATION
CRISPR-DO for genome-wide CRISPR design and optimization
- Authors
- Ma, J., Köster, J., Qin, Q., Hu, S., Li, W., Chen, C., Cao, Q., Wang, J., Mei, S., Liu, Q., Xu, H., Liu, X.S.
- ID
- ZDB-PUB-160713-5
- Date
- 2016
- Source
- Bioinformatics (Oxford, England) 32(21): 3336-3338 (Journal)
- Registered Authors
- Li, Wei
- Keywords
- none
- MeSH Terms
-
- Animals
- Clustered Regularly Interspaced Short Palindromic Repeats*
- Computational Biology*
- DNA
- Exons
- Gene Editing*
- Genome*
- Humans
- Mice
- RNA, Guide, Kinetoplastida
- PubMed
- 27402906 Full text @ Bioinformatics
Citation
Ma, J., Köster, J., Qin, Q., Hu, S., Li, W., Chen, C., Cao, Q., Wang, J., Mei, S., Liu, Q., Xu, H., Liu, X.S. (2016) CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics (Oxford, England). 32(21):3336-3338.
Abstract
Motivation Despite the growing popularity in using CRISPR/Cas9 technology for genome editing and gene knockout, its performance still relies on well designed single guide RNAs (sgRNA). In this study, we propose a web application for the Design and Optimization (CRISPR-DO) of guide sequences that target both coding and non-coding regions in spCas9 CRISPR system across human, mouse, zebrafish, fly and worm genomes. CRISPR-DO uses a computational sequence model to predict sgRNA efficiency, and employs a specificity scoring function to evaluate the potential of off-target effect. It also provides information on functional conservation of target sequences, as well as the overlaps with exons, putative regulatory sequences and single nucleotide polymorphisms (SNP). The web application has a user-friendly genome-browser interface to facilitate the selection of the best target DNA sequences for experimental design.
Availability CRISPR-DO is available at http://cistrome.org/crispr/ CONTACT: qiliu@tongji.edu.cn, hanxu@jimmy.harvard.edu, xsliu@jimmy.harvard.edu.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping