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- Kornel Labun
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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- Tessa G Montague
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
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- Maximilian Krause
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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- Yamila N Torres Cleuren
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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- Håkon Tjeldnes
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
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- Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5008 Bergen, Norway
説明
<jats:title>Abstract</jats:title> <jats:p>The CRISPR–Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR–Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.no</jats:p>
収録刊行物
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- Nucleic Acids Research
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Nucleic Acids Research 47 (W1), W171-W174, 2019-05-20
Oxford University Press (OUP)