Tools for CRISPR/CAS9

Question

[Jimpix]

Hi!

Which bioinformatics tools supporting CRISPR-Cas Experiments do you recommend? Or which tools are you using?

[Jimpix]

all application, which tools are the most used

Answer 1

[Mohammad Reza Bakhtiarizadeh]

Hi You can try our package in R, Casilico. It supports Cas12, Cas13, and Cas14 CRISPR-Cas systems. Using a list of important features such as mismatch tolerance rules, self-complementarity, GC content, frequency of cleaving base around the target site, target accessibility and PFS (protospacer flanking site) or PAM (protospacer adjacent motif) requirement, CaSilico searches all potential crRNAs in a user-input sequence.

CaSilico outperforms previous crRNA design tools in the following respects: 1) supporting any reference genome/transcriptome for which a FASTA file is available; 2) designing crRNAs that simultaneously target multiple sequences through conserved region detection among a set of sequences; 3) considering new CRISPR-Cas subtypes; 4) reporting a list of different features for each candidate crRNA, which can help the user to select the best one. Our paper was puplished in Frontiers in Bioengineering and Biotechnology.

Our tool is sufficiently flexible to tune some key parameters governing the design of crRNA and identification of off-targets, which can be led to increases the chances of successful CRISPR-Cas experiments. Given these capabilities, Casilico addresses end-user concerns arising from the use of sophisticated bioinformatics algorithms and has a wide range of potential research applications in different areas especially design of crRNA for pathogen diagnosis. Casilico was successfully applied to design crRNAs for different genes in SARS-CoV-2 genome, as some of the crRNAs have been experimentally tested in the previous studies.

[AfredJackson2015]

Hi, I think CaSilico is the best choose for me. I'll try it. Thanks so much!

Answer 2

[Michael]

Here is CHOPCHOP which has been developed at our institute. It supports different approaches (Cas9, Cas13, Cpf1, TALEN) and knock-out, knock-in, activation, and repression.

And here is a more comprehensive list of all CRISPR tools in bio.tools sorted by citations, as in "most used successfully".

[AfredJackson2015]

I want to design crRNA for multiple strains of a virus for Cas13 but is not possible with CHOPCHOP? What should I do?

[Michael]

The genomes of the viral strains may have to be added to the tool before you can use them. Instructions for adding genomes is given here: https://chopchop.cbu.uib.no/submissions You can also contact the authors via the email address given on that web page about your use case.

[AfredJackson2015]

Actually, I'm going to design a crRNA to target all these strains, something like targeting conserved regions on these genomes.

[Michael]

hi. Basically, CHOPCHOP can not be used to design crRNAs for CRISPR Cas systems like Cas13, as it is restricted to only two organisms (Human and mouse). Also, it does not support off-targets analysis. Also, it can not design crRNAs to target multiple targets/sequences simultaneously.