Flask Parent Template

Get a complete CRISPR plan for your point mutation request

The Automated CRISPR Planner aims to streamline your CRISPR design process given only the gene name and the amino acid mutation you wish to insert.

The tool is designed for point mutations (one amino acid changed to another) in the Caenorhabditis elegans genome.
The tool has been built to generate CRISPR designs according to the methods described in Alexandre Paix and Geraldine Seydoux's paper:

Paix, A., Folkmann, A., & Seydoux, G. (2017). Precision genome editing using CRISPR-Cas9 and linear repair templates in C.elegans. Methods, 121, 86-93.

Automated CRISPR Planner

Please insert your worm gene name, amino acid site you wish to mutate, the original amino acid you wish to alter and the new amino acid you wish to introduce.
You can insert the nucleotide strand sequence (unspliced + UTR) yourself or leave it empty and the program will extract the sequence from other sources.

If you don't have a valid crRNA sequence with which you wish to plan your CRISPR, please leave that box empty.
After clicking the "Submit" button, you will be presented with all possible crRNA sequences relevant to your request.
In order to get results regarding a crRNA sequence of your choosing, copy the crRNA (and remember its strand), and re-fill your query, this time attaching the chosen crRNA.

Your worm gene name:
The amino acid site:
The isoform full name (optional) :
For example: PDR-1 gene has 3 different isoforms: K08E3.7a.1 , K08E3.7b.1 , K08E3.7b.2 , K08E3.7c.1.
insert full isoform name as written in WormBase.
The nucleotide strand (unspliced + UTR; optional):
From: To:
Preferred restriction enzymes (no need to add the notation "-HF" for high fidelity):
For example: EcoRI, PvuII, BspHI, etc'.
*By not providing any relevant restriction enzymes, the tool will search for all known enzymes.
Maximum number of results (per crRNA)
chosen crRNA (if you have already): in strand:

***The process can take up to several minutes, please be patient***