CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.
Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5' end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a...
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doaj-158dd8d38dce4fb7b5fcd241086df48b2020-11-25T01:24:04ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01104e012463310.1371/journal.pone.0124633CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.Manuel StemmerThomas ThumbergerMaria Del Sol KeyerJoachim WittbrodtJuan L MateoEngineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5' end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de) to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites.http://europepmc.org/articles/PMC4409221?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Manuel Stemmer Thomas Thumberger Maria Del Sol Keyer Joachim Wittbrodt Juan L Mateo |
spellingShingle |
Manuel Stemmer Thomas Thumberger Maria Del Sol Keyer Joachim Wittbrodt Juan L Mateo CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS ONE |
author_facet |
Manuel Stemmer Thomas Thumberger Maria Del Sol Keyer Joachim Wittbrodt Juan L Mateo |
author_sort |
Manuel Stemmer |
title |
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. |
title_short |
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. |
title_full |
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. |
title_fullStr |
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. |
title_full_unstemmed |
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. |
title_sort |
cctop: an intuitive, flexible and reliable crispr/cas9 target prediction tool. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2015-01-01 |
description |
Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5' end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de) to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites. |
url |
http://europepmc.org/articles/PMC4409221?pdf=render |
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