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CRISPR Guide RNA Design

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.
CRISPR gRNA design tool
CRISPR gRNA sequence import and annotation

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
CRISPR gRNA specificity scoring

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
Large batch gRNA design tool

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 competitors
CRISPR gRNA sequence - save and export

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

“What Benchling has provided us is a single solution for multiple different problems, from sequence design and alignment to a centralized database. Our speed has doubled, communication has improved exponentially, and it's decreased scientist frustration level beyond measure.”

Brenda Minesinger
Principal Scientist, Intellia Therapeutics

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