Nucleic acids researchMay 12, 2016

Interactive design of guide RNAs for CRISPR-Cas experiments using ENSEMBL genomes

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗OA ↗

Updated Mar 31, 2026

Abstract

The Breaking-Cas system allows for the design of guide RNAs for CRISPR/Cas experiments using approximately 700 eukaryotic genomes.

Guide RNAs direct nucleases to specific genomic locations and must avoid off-target effects.
Breaking-Cas features unique capabilities, including adjustable PAM sequences and customizable guide RNA lengths.
The system supports various types of CRISPR/Cas experiments, including those using the Cas9 nuclease.
Access to the Breaking-Cas server is free for users, with the underlying code available upon request.

Simplified

The CRISPR/Cas technology is enabling targeted genome editing in multiple organisms with unprecedented accuracy and specificity by using RNA-guided nucleases. A critical point when planning a CRISPR/Cas experiment is the design of the guide RNA (gRNA), which directs the nuclease and associated machinery to the desired genomic location. This gRNA has to fulfil the requirements of the nuclease and lack homology with other genome sites that could lead to off-target effects. Here we introduce the Breaking-Cas system for the design of gRNAs for CRISPR/Cas experiments, including those based in the Cas9 nuclease as well as others recently introduced. The server has unique features not available in other tools, including the possibility of using all eukaryotic genomes available in ENSEMBL (currently around 700), placing variable PAM sequences at 5' or 3' and setting the guide RNA length and the scores per nucleotides. It can be freely accessed at: http://bioinfogp.cnb.csic.es/tools/breakingcas, and the code is available upon request.

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Interactive design of guide RNAs for CRISPR-Cas experiments using ENSEMBL genomes

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