AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
Abstract 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-s...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-019-1783-3 |
| _version_ | 1819205473594769408 |
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| author | Kathleen C. Keough Svetlana Lyalina Michael P. Olvera Sean Whalen Bruce R. Conklin Katherine S. Pollard |
| author_facet | Kathleen C. Keough Svetlana Lyalina Michael P. Olvera Sean Whalen Bruce R. Conklin Katherine S. Pollard |
| author_sort | Kathleen C. Keough |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-23T04:52:16Z |
| format | Article |
| id | doaj.art-caf4e3785dd3473b8d998fce0a68e119 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-23T04:52:16Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-caf4e3785dd3473b8d998fce0a68e1192022-12-21T17:59:26ZengBMCGenome Biology1474-760X2019-08-012011910.1186/s13059-019-1783-3AlleleAnalyzer: a tool for personalized and allele-specific sgRNA designKathleen C. Keough0Svetlana Lyalina1Michael P. Olvera2Sean Whalen3Bruce R. Conklin4Katherine S. Pollard5Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of CaliforniaGladstone InstitutesGladstone InstitutesGladstone InstitutesGladstone InstitutesGladstone InstitutesAbstract 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.http://link.springer.com/article/10.1186/s13059-019-1783-3CRISPRsgRNA designGenomicsGenome surgeryGenome editingComputational biology |
| spellingShingle | Kathleen C. Keough Svetlana Lyalina Michael P. Olvera Sean Whalen Bruce R. Conklin Katherine S. Pollard AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design Genome Biology CRISPR sgRNA design Genomics Genome surgery Genome editing Computational biology |
| 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 | CRISPR sgRNA design Genomics Genome surgery Genome editing Computational biology |
| url | http://link.springer.com/article/10.1186/s13059-019-1783-3 |
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