CRISPR Primer Designer： Design primers for knockout and chromosome imaging CRISPR-Cas system
The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about...
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| Published in | Journal of integrative plant biology Vol. 57; no. 7; pp. 613 - 617 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
China (Republic : 1949- )
Blackwell Publishing Ltd
01.07.2015
National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences,Shanghai 200032, China |
| Subjects | |
| Online Access | Get full text |
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| Abstract | The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user- friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present researchers to design primers CRISPR Primer Designer for for CRISPR applications. Theprogram has a user-frfendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRiSPR-Cas system-based chromosome imaging system. |
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| AbstractList | The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system.The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system. The clustered regularly interspaced short palin-dromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especial y the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran local y and acquired a user-friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were stil no tools helping users to generate specific end-user spacers. We herein present CRISPR Primer Designer for researchers to design primers for CRISPR applications. The program has a user-friendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs local y and can be used to search spacer clusters, and exports primers for the CRISPR-Cas system-based chromosome imaging system. The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user- friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present researchers to design primers CRISPR Primer Designer for for CRISPR applications. Theprogram has a user-frfendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRiSPR-Cas system-based chromosome imaging system. |
| Author | Meng Yan Shi-Rong Zhou Hong-Wei Xue |
| AuthorAffiliation | National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, Shanghai 200032., China |
| AuthorAffiliation_xml | – name: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences,Shanghai 200032, China |
| Author_xml | – sequence: 1 givenname: Meng surname: Yan fullname: Yan, Meng organization: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, 200032, Shanghai, China – sequence: 2 givenname: Shi-Rong surname: Zhou fullname: Zhou, Shi-Rong email: srzhou@sibs.ac.cnhwxue@sibs.ac.cn organization: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, 200032, Shanghai, China – sequence: 3 givenname: Hong-Wei surname: Xue fullname: Xue, Hong-Wei email: srzhou@sibs.ac.cnhwxue@sibs.ac.cn organization: National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences, 200032, Shanghai, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25319067$$D View this record in MEDLINE/PubMed |
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| Copyright | 2014 Institute of Botany, Chinese Academy of Sciences 2014 Institute of Botany, Chinese Academy of Sciences. Copyright © Wanfang Data Co. Ltd. All Rights Reserved. |
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| DocumentTitleAlternate | CRISPR Primer Designer： Design primers for knockout and chromosome imaging CRISPR-Cas system |
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| GrantInformation_xml | – fundername: Chinese Academy of Sciences – fundername: We would like to thank Zheng-Yan Feng from Shanghai Stress Biology Center, CAS, for the specificity of the CRISPR-Cas system and CRISPR protocol in the help system. This study was supported by the State Key Project of Basic Research; SIBS; the Knowledge Innovation Program of the Chinese Academy of Sciences funderid: (2012CB944804); (2013KIP105); (KSCX3-EW-N-01) |
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| Keywords | knockout CRISPR software primer Chromosome imaging |
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| Notes | 11-5067/Q Chromosome imaging; CRISPR; knockout; primer; software The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user- friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present researchers to design primers CRISPR Primer Designer for for CRISPR applications. Theprogram has a user-frfendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRiSPR-Cas system-based chromosome imaging system. Chinese Academy of Sciences istex:E25B9B4D4C9859800749BCBCFC9CB0B4198F864B ark:/67375/WNG-5PJPKW3F-P ArticleID:JIPB12295 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
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| PublicationTitle | Journal of integrative plant biology |
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| Publisher | Blackwell Publishing Ltd National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, the Chinese Academy of Sciences,Shanghai 200032, China |
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| Snippet | The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful... The clustered regularly interspaced short palindromic repeats (CRISPR)‐associated system enables biologists to edit genomes precisely and provides a powerful... The clustered regularly interspaced short palindromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful... The clustered regularly interspaced short palin-dromic repeats (CRISPR)-associated system enables biologists to edit genomes precisely and provides a powerful... |
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| SubjectTerms | biologists Cas系统 Chromosome imaging chromosomes Chromosomes, Plant - genetics Clustered Regularly Interspaced Short Palindromic Repeats - genetics CRISPR CRISPR-Cas Systems - genetics DNA Primers - metabolism epigenetics Gene Knockout Techniques genes image analysis Imaging, Three-Dimensional Internet knockout plasmids primer researchers Software 基因敲除 基因组结构 多参数分析 引物设计 成像系统 染色体 设计工具 |
| Title | CRISPR Primer Designer： Design primers for knockout and chromosome imaging CRISPR-Cas system |
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