Journal
BIOINFORMATICS
Volume 32, Issue 21, Pages 3336-3338Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btw476
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Funding
- National Natural Science Foundation of China [31329003]
- NIH [R01 HG008728]
- Claudia Adams Barr Award in Innovative Basic Cancer Research from Dana-Farber Cancer Institute
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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 (SNPs). The web application has a user-friendly genome-browser interface to facilitate the selection of the best target DNA sequences for experimental design.
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