E-CRISP: Design of custom gRNA constructs
Posted by Florian Heigwer, on 30 August 2013
E-CRISP is now available under: www.e-crisp.org
Genome editing by applying the CRISPR/Cas system has been shown to be a promising new tool in genetics. CRISPR/Cas works by guided DNA double strand breaks (DSB) at specific loci in the genomic or exogenic DNA, where various kinds of sequence alterations can be introduced (exploiting the cellular DSB-repair machinery). As the CRISPR/Cas system is rapidly developing, it remains important to systematically assess which design parameters/properties of CRISPR/Cas constructs influence experimental outcome.
Bioinformatics methods can be used to find suitable target sites for the DSB in a systematic manner. We developed E-CRISP to design CRISPR constructs and provide the possibility to alter various design parameters systematically. A fast nucleotide indexing approach and the application of a binary interval tree for construct annotation make E-CRISP very fast.
Until now E-CRISP is available for eight different organisms, including mouse, rat, fish, fly, worm, Arabidopsis, yeast and human, providing the possibility to use it for different model organisms. This list is easily extendable upon request.
The only information needed to design a CRISPR with this application, is the organism of interest and the target gene-symbol or sequence. Default parameters can be used or adapted to suit the particular needs. E-CRISP identifies and evaluates potential CRISPR targets by a combination of options including specificity (should target one locus only), nucleotide composition, experimental purpose and genomic context (if it targets a gene, which exon, lies in CpG island) among others.
Additionally, E-CRISP offers a re-evaluation tool to identify and annotate targets of CRISPR constructs designed by other sources (or designed by E-CRISP itself).