1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Casilico: A versatile CRISPR package for in silico CRISPR RNA designing
Paper ID : 1113-ICB10
Authors:
Adnan Asadbagi1, Milad Norouzi1, Mohammad sadegh Vafaei sadi1, Mojtaba Saffari2, Mohammad Reza Bakhtiarizadeh *3
1دانشگاه تهران
2Tehran University of Medical Sciences
3University of Tehran
Abstract:
Background
The efficiency of CRISPR-Cas system is highly depends on well-designed CRISPR RNA (crRNA). To facilitate the use of various types of CRISPR-Cas systems, there is a need for development of computational tools to design crRNAs which cover different CRISPR-Cas systems with off-target analysis capability. Numerous crRNA design tools have been developed but nearly all of them are dedicated to design crRNA for genome editing. Hence, we developed a tool matching the needs of both beginners and experts, named Casilico, which was inspired by the limitations of the current gRNA design tools for designing crRNAs for Cas12, Cas13, and Cas14 CRISPR-Cas systems [3,4].

Materials and Methods
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 protospacer flanking site or protospacer adjacent motif requirement [1,2], Casilico searches all potential crRNAs in a user-input sequence. Considering these features, help users to rank all crRNAs for a sequence and make an informed decision about whether a crRNA is suited for an experiment or not. Our tool is sufficiently flexible to tune some key parameters governing the design of crRNA and identification of off-targets, led to increases the chances of successful CRISPR-Cas experiments.

Results, and Conclusion
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. 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 [5,6].
Keywords:
Cas13, Cas12, Cas14, Guide RNA, CRISPR Cas
Status : Paper Accepted (Oral Presentation)