CRISPR Guide RNA Design Tool

The CRISPR Guide RNA design tool allows you to visualize, optimize, and annotate multiple gRNA sequences at a time. Get on and off-target scores in seconds to compare and optimize for higher activity and lower off-target effects. Save, organize and attach guides to relevant sequences and assemble gRNAs into plasmids — all within Benchling.

Import your target region, fully annotated

Specify a gene or genome coordinates, and Benchling will automatically annotate it with the exon and CDS information you need to design guides
Import directly from 160+ reference genomes
Import your own sequence of any common file type

Score your gRNAs by specificity and efficiency

Benchling uses the latest algorithms to instantly assess off-target effects and on-target efficiency for your guides
Browse your sequence while examining scores to find the best guides in important domains of a gene

The only software for large batch gRNA design

Need to design hundreds of guides at once? Benchling's CRISPR tool eliminates tedious work by batching gRNA design and executing it up to 100x faster than leading competitor

Save and export guide sequences

Save your guides as oligos on Benchling, organize them using tags and folders, and clone them into CRISPR plasmids
Alternatively, export your guides, along with scores and off-target sites, for easy use in other tools

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