CRISPRware：用于上下文gRNA库设计的软件包。

IF 3.7 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

BMC Genomics Pub Date : 2025-07-01 DOI:10.1186/s12864-025-11775-8

Eric Malekos, Christy Montano, Susan Carpenter

{"title":"CRISPRware：用于上下文gRNA库设计的软件包。","authors":"Eric Malekos, Christy Montano, Susan Carpenter","doi":"10.1186/s12864-025-11775-8","DOIUrl":null,"url":null,"abstract":"We present CRISPRware, an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages next-generation sequencing data to design context-specific gRNAs and can account for genetic variation, which allows allele-specific guide design on a genome-wide scale. As a demonstration of use and to create a publicly available resource, we use CRISPRware to identify and score gRNAs against coding sequences in six model organisms for Cas9 and Cas12A and host these in a publicly available session on the UCSC Genome Browser.","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"607"},"PeriodicalIF":3.7000,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210694/pdf/","citationCount":"0","resultStr":"{\"title\":\"CRISPRware: a software package for contextual gRNA library design.\",\"authors\":\"Eric Malekos, Christy Montano, Susan Carpenter\",\"doi\":\"10.1186/s12864-025-11775-8\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"We present CRISPRware, an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages next-generation sequencing data to design context-specific gRNAs and can account for genetic variation, which allows allele-specific guide design on a genome-wide scale. As a demonstration of use and to create a publicly available resource, we use CRISPRware to identify and score gRNAs against coding sequences in six model organisms for Cas9 and Cas12A and host these in a publicly available session on the UCSC Genome Browser.\",\"PeriodicalId\":9030,\"journal\":{\"name\":\"BMC Genomics\",\"volume\":\"26 1\",\"pages\":\"607\"},\"PeriodicalIF\":3.7000,\"publicationDate\":\"2025-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210694/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"BMC Genomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s12864-025-11775-8\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Genomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12864-025-11775-8","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}

引用次数: 0

摘要

我们提出了CRISPRware，一种针对转录、翻译和非编码区域生成引导RNA （gRNA）文库的有效方法。CRISPRware利用下一代测序数据来设计上下文特异性grna，并可以解释遗传变异，从而允许在全基因组范围内进行等位基因特异性指导设计。为了演示使用并创建一个公开可用的资源，我们使用CRISPRware在六种模式生物中针对Cas9和Cas12A的编码序列识别和评分grna，并在UCSC基因组浏览器的公开可用会话中托管这些grna。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

CRISPRware: a software package for contextual gRNA library design.

We present CRISPRware, an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages next-generation sequencing data to design context-specific gRNAs and can account for genetic variation, which allows allele-specific guide design on a genome-wide scale. As a demonstration of use and to create a publicly available resource, we use CRISPRware to identify and score gRNAs against coding sequences in six model organisms for Cas9 and Cas12A and host these in a publicly available session on the UCSC Genome Browser.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

BMC Genomics 生物-生物工程与应用微生物

CiteScore

7.40

自引率

4.50%

发文量

769

审稿时长

6.4 months

期刊介绍： BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.