The CRISPR-Cas9 genome editing has many advantages over its counterparts and could ultimately assist in disease control and molecular breeding in aquaculture.Single-guide RNA(sgRNA)design is presumably the most crucia...The CRISPR-Cas9 genome editing has many advantages over its counterparts and could ultimately assist in disease control and molecular breeding in aquaculture.Single-guide RNA(sgRNA)design is presumably the most crucial task in a typical CRISPR-Cas9 experiment;an understanding of algorithms behind sgRNA design programs is thus essential for improved efficacy and specificity.We focus this review on the bioinformatics aspects in genome editing experiments and describe commonly used computational approaches and tools of sgRNA design and outcome assessment.We show an example of sgRNA design with optimal parameter settings and appropriate interpretation of results and present a brief overview of CRISPR-Cas9 applications,such as genetic improvement and sustainability in aquaculture.We discuss challenging issues,particularly in the context of computational biology,in the use of computational tools in CRISPR-based genome editing.This review provides a synthesis of bioinformatics tools used for CRISPR-Cas9 sgRNA design and outcome assessment and offers a general view of CRISPR-based applications in farmed fish,which are expected to facilitate genome editing programs and hence improve aquaculture breeding,production,and sustainability.展开更多
CRISPR-mediated gene-editing technology has arguably driven an unprecedented revolution in biological sciences for its role in elucidating gene functions.A multitude of software has been developed for the design and a...CRISPR-mediated gene-editing technology has arguably driven an unprecedented revolution in biological sciences for its role in elucidating gene functions.A multitude of software has been developed for the design and analysis of CRISPR/Cas experiments,including predictive tools to design optimally guide RNA for various experimental operations.Different in silico sgRNA design tools have various application scenarios and identifying the optimal design tools can often be a challenge.This paper describes the sgRNA design workflow in experiments,the classification of sgRNA designers,previously published benchmarking work of in silico designers,and the criteria involved how to select an sgRNA web server.Through basic testing,this paper comprehensively overviews and compares the features of 43 web server designers to provide a reference for the readers.Ultimately,the project developed an integrated platform,called Aid-TG,which helps users find appropriate tools quickly.展开更多
基金This publication was made possible through funding support from the National Science Foundation(DBI-1919574)and the University of Nebraska at Omaha.
文摘The CRISPR-Cas9 genome editing has many advantages over its counterparts and could ultimately assist in disease control and molecular breeding in aquaculture.Single-guide RNA(sgRNA)design is presumably the most crucial task in a typical CRISPR-Cas9 experiment;an understanding of algorithms behind sgRNA design programs is thus essential for improved efficacy and specificity.We focus this review on the bioinformatics aspects in genome editing experiments and describe commonly used computational approaches and tools of sgRNA design and outcome assessment.We show an example of sgRNA design with optimal parameter settings and appropriate interpretation of results and present a brief overview of CRISPR-Cas9 applications,such as genetic improvement and sustainability in aquaculture.We discuss challenging issues,particularly in the context of computational biology,in the use of computational tools in CRISPR-based genome editing.This review provides a synthesis of bioinformatics tools used for CRISPR-Cas9 sgRNA design and outcome assessment and offers a general view of CRISPR-based applications in farmed fish,which are expected to facilitate genome editing programs and hence improve aquaculture breeding,production,and sustainability.
文摘CRISPR-mediated gene-editing technology has arguably driven an unprecedented revolution in biological sciences for its role in elucidating gene functions.A multitude of software has been developed for the design and analysis of CRISPR/Cas experiments,including predictive tools to design optimally guide RNA for various experimental operations.Different in silico sgRNA design tools have various application scenarios and identifying the optimal design tools can often be a challenge.This paper describes the sgRNA design workflow in experiments,the classification of sgRNA designers,previously published benchmarking work of in silico designers,and the criteria involved how to select an sgRNA web server.Through basic testing,this paper comprehensively overviews and compares the features of 43 web server designers to provide a reference for the readers.Ultimately,the project developed an integrated platform,called Aid-TG,which helps users find appropriate tools quickly.
