Comparison of two computational online tools for sgRNA designing in gene editing experiments by CRISPR/Cas۹

Background: CRISPR/Cas۹ system is a specific genetic manipulation method that causes thespecific double stranded break (DSB). The sgRNA sequence plays a fundamental role to successwith high efficiency through limiting off-target cutting. There are several softwares that can beused to predict sgRNA primers with different efficiency and specificity for cutting target sites.Each software has some advantages and limitations that should be considered in sgRNA design.Here, we compared two standard tools with different algorithms, EuPaGDT and CRISPOR,which are common software in eukaryotic cells.Materials and Methods: First, we found more than ۱۰ leishmanial specific gene sequences fromdifferent species from tritrypDB database and then, we tried to predict the best sgRNA sequencesthrough two different algorithms.Results: Both softwares identified common specific sgRNA sequences but their efficiency scoreand off-target sites predicted with very different. CRISPOR was able to detect both intergenicand intragenic off-targets with more power than EuPaGDT. In spite of the number of predictedprimers were equal in both software but CRISPOR put the almost ۷۰% of itself predictionsgRNA primers in high score cluster but EuPaGDT high score data contain nearly ۶۰% of allprimers and just about ۴۰% of high efficiency score primers were similar in both of them for allgenes.Conclusion: Both softwares are strong approach for prediction of sgRNA. Nevertheless, using ofseveral software to determine the best sgRNA for gene knockout or tagging, and also, sometimesusing of more than one guide primers with high scores is recommended.

کلیدواژه ها:

CRISPR/Cas۹ ، sgRNA ، CRISPOR ، EuPaGDT