AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is an open-source sof...

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Autores principales: Keough, Kathleen C., Lyalina, Svetlana, Olvera, Michael P., Whalen, Sean, Conklin, Bruce R., Pollard, Katherine S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694686/
https://www.ncbi.nlm.nih.gov/pubmed/31416467
http://dx.doi.org/10.1186/s13059-019-1783-3
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author Keough, Kathleen C.
Lyalina, Svetlana
Olvera, Michael P.
Whalen, Sean
Conklin, Bruce R.
Pollard, Katherine S.
author_facet Keough, Kathleen C.
Lyalina, Svetlana
Olvera, Michael P.
Whalen, Sean
Conklin, Bruce R.
Pollard, Katherine S.
author_sort Keough, Kathleen C.
collection PubMed
description The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is an open-source software that incorporates single-nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing 1 or multiple haplotypes of a sequenced genome, currently supporting 11 Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at https://github.com/keoughkath/AlleleAnalyzer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1783-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-66946862019-08-19 AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design Keough, Kathleen C. Lyalina, Svetlana Olvera, Michael P. Whalen, Sean Conklin, Bruce R. Pollard, Katherine S. Genome Biol Method The CRISPR/Cas system is a highly specific genome editing tool capable of distinguishing alleles differing by even a single base pair. Target sites might carry genetic variations that are not distinguishable by sgRNA designing tools based on one reference genome. AlleleAnalyzer is an open-source software that incorporates single-nucleotide variants and short insertions and deletions to design sgRNAs for precisely editing 1 or multiple haplotypes of a sequenced genome, currently supporting 11 Cas proteins. It also leverages patterns of shared genetic variation to optimize sgRNA design for different human populations. AlleleAnalyzer is available at https://github.com/keoughkath/AlleleAnalyzer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1783-3) contains supplementary material, which is available to authorized users. BioMed Central 2019-08-15 /pmc/articles/PMC6694686/ /pubmed/31416467 http://dx.doi.org/10.1186/s13059-019-1783-3 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Keough, Kathleen C.
Lyalina, Svetlana
Olvera, Michael P.
Whalen, Sean
Conklin, Bruce R.
Pollard, Katherine S.
AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
title AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
title_full AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
title_fullStr AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
title_full_unstemmed AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
title_short AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
title_sort alleleanalyzer: a tool for personalized and allele-specific sgrna design
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694686/
https://www.ncbi.nlm.nih.gov/pubmed/31416467
http://dx.doi.org/10.1186/s13059-019-1783-3
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