CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants

Abstract The off-target effect, in which DNA cleavage was conducted outside the targeted region, is a major problem which limits the applications of CRISPR/Cas9 genome editing system. CRISPR Off-target Predictor (CROP) is standalone program developed to address this problem by predicting off-target...

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Autores principales:	Victor Aprilyanto, Redi Aditama, Zulfikar Achmad Tanjung, Condro Utomo, Tony Liwang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3eb2522a7bed476db29ca112e577cb88
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spelling	oai:doaj.org-article:3eb2522a7bed476db29ca112e577cb882021-12-02T15:23:09ZCROP: a CRISPR/Cas9 guide selection program based on mapping guide variants10.1038/s41598-021-81297-22045-2322https://doaj.org/article/3eb2522a7bed476db29ca112e577cb882021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-81297-2https://doaj.org/toc/2045-2322Abstract The off-target effect, in which DNA cleavage was conducted outside the targeted region, is a major problem which limits the applications of CRISPR/Cas9 genome editing system. CRISPR Off-target Predictor (CROP) is standalone program developed to address this problem by predicting off-target propensity of guide RNAs and thereby allowing the user to select the optimum guides. The approach used by CROP involves generating substitution, deletion and insertion combinations which are then mapped into the reference genome. Based on these mapped variants, scoring and alignment are conducted and then reported as a table comprising the off-target propensity of all guide RNAs from a given gene sequence. The Python script for this program is freely available from: https://github.com/vaprilyanto/crop .Victor AprilyantoRedi AditamaZulfikar Achmad TanjungCondro UtomoTony LiwangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Victor Aprilyanto Redi Aditama Zulfikar Achmad Tanjung Condro Utomo Tony Liwang CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
description	Abstract The off-target effect, in which DNA cleavage was conducted outside the targeted region, is a major problem which limits the applications of CRISPR/Cas9 genome editing system. CRISPR Off-target Predictor (CROP) is standalone program developed to address this problem by predicting off-target propensity of guide RNAs and thereby allowing the user to select the optimum guides. The approach used by CROP involves generating substitution, deletion and insertion combinations which are then mapped into the reference genome. Based on these mapped variants, scoring and alignment are conducted and then reported as a table comprising the off-target propensity of all guide RNAs from a given gene sequence. The Python script for this program is freely available from: https://github.com/vaprilyanto/crop .
format	article
author	Victor Aprilyanto Redi Aditama Zulfikar Achmad Tanjung Condro Utomo Tony Liwang
author_facet	Victor Aprilyanto Redi Aditama Zulfikar Achmad Tanjung Condro Utomo Tony Liwang
author_sort	Victor Aprilyanto
title	CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
title_short	CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
title_full	CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
title_fullStr	CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
title_full_unstemmed	CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
title_sort	crop: a crispr/cas9 guide selection program based on mapping guide variants
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/3eb2522a7bed476db29ca112e577cb88
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CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants

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