1.theuniverseofCRISPRCassequencesCRISPR-Cas序列的建模。 CRISPR相关蛋白语言模型 Cas9蛋白语言模型 指导RNA设计模型 基因编辑的产生 蛋白质生成受限。 用于表征的蛋白质的选择 sgRNA的设计 用于基础编辑的deaminases的设计 基因编辑器的特性 原文: Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences | bioRhttps://blog.csdn.net/weixin_46120256/article/details/138635902

2.研究人员建立蛋白工程化改造新方法和基于Cas12i的基因编辑新工具CRISPR-Cas基因组编辑技术在基因治疗、农作物经济性状改良及基础研究等领域均有多样化的应用，引领生物技术与应用的快速发展。自然界中广泛存在的天然CRISPR-Cas系统为新型基因编辑工具研发提供了丰富资源。然而，自然界微生物中发现的大多数Cas工具蛋白在哺乳动物细胞中的编辑效率较低，这限制了它们的应用，尤其是在生物https://baijiahao.baidu.com/s?id=1734341538486314607&wfr=spider&for=pc

3.CIDPCRISPRsgRNA设计模块CRISPR的重要性和应用前景,不需要再多罗嗦了。在CRISPR整个系统中,sgRNA是引导切割酶到达基因组指定位置的中间媒介,就是它负责识别目的基因进而发挥CRISPR切割等作用的。因而,sgRNA的设计是应用CRISPR系统的前提和关键。我整理了目前所能找到的26款sgRNA设计软件,其中有22款软件是需要用户选择背景数据集(即背景物种,通常https://www.jianshu.com/p/202f198fb188

4.CRISPRoffinder:aCRISPRguideRNAdesignandoffHowever, most of these tools can only design sgRNAs for the CRISPR/Cas system. In this study, a user-friendly standalone program named “CRISPR-offinder” was developed to provide researchers a tool for quick design of sgRNAs with minimal off-target effects for different CRISPR systems, https://www.ijbs.com/v13p1470.htm

5.CRISPRGuideDesignToolsandAlgorithmSTEMCELLTechnologiesThe CRISPR Guide Design Tool uses best practices and the latest computational tools to deliver the optimal CRISPR RNA (crRNA) or single guide RNA (sgRNA) sequence for every gene in the human and mouse genomes. Access the CRISPR Design Tools https://www.stemcell.com/crispr-guide-design-algorithm

6.CRISPRgRNADesigntoolCRISPR gRNA Design tool lets you design gRNA(s) to efficiently engineer your target and minimize off-target effects using ATUM Scoring Algorithms.https://www.atum.bio/eCommerce/cas9/input

7.CRISPRDesign custom gRNA CRISPR-Cas9 gRNA checker Species Input format Paste/Type input Upload file Enter up to 99 FASTA Sequences. Please enter sequences in standard FASTA formatting. This field is required. IDT RUO products are manufactured in accordance with ISO 9001 and are intended for research https://www.idtdna.com/site/order/designtool/index/CRISPR_SEQUENCE

8.pfcellsCRISPR Design Tool World’s Fastest & Easiest CRISPR Gene Knockout Design Tool Launch Design Tool Bioinformatics Tools CRISPR Design Tool OverviewBenefitsDataLaunch Overview The Best CRISPR Design Tool for Knockouts. Our powerful CRISPR software simplifies gRNA design. Choose from over 120,000 genomes http://www.synthego.com/products/bioinformatics/crispr-design-tool

9.engineeringusinganorthogonaltriwe followed the previously developed HI-CRISPR design20, where the homology donor sequences were integrated into the gRNA expression cassette. We found that the stable maintenance of the homology donor resulted in a further increase in CRISPRd efficiency: from 80% with Sg10 (Table1) to ~?98https://www.nature.com/articles/s41467-017-01695-x

10.CRISPRCRISPR-Cas9 sgRNA design and construction Single guided RNAs (sgRNA) targeting exons 29–30 of ITGA2 were designed using the web tool of UCSC Genome browser (https://genome.ucsc.edu/). The selected gRNAs were fulfilled the requirement as MIT guide specificity >60, high predicted cleavage https://bio-protocol.org/mv2/prep600

11.GitHubBase functions and classes for CRISPR gRNA design. Contribute to crisprVerse/crisprBase development by creating an account on GitHub.https://github.com/crisprVerse/crisprBase

12.EE-CRISP Design of CRISPR constructs Check out our new CRISPR Library Designer (CLD): batch design of sgRNA libraries Download the dockerized version now atCLD on Github 1. Select organism: [HELP] 2. Select target region by gene symbol or sequence: http://www.e-crisp.org/

13.CRISPRgRNA(guideRNA)DesignToolforEukaryoticPathogensbatch mode available here Gene tagging batch mode available here(?) Our CRISPR/Cas gRNA design tool has a new look!! Job Name: RNA guided nuclease selection:(?) SpCas9: 20nt gRNA, NGG PAM on 3' endSaCas9: 21nt gRNA, NNGRRT PAM on 3' endAsCpf1: 20nt gRNA, TTTN PAM on 5' endhttp://grna.ctegd.uga.edu/

14.DECKO:Singleoligo,dualDual excision CRISPR knockout design CRISPR can be used to delete genomic sequences, by cutting genomic DNA at two sites and relying on non-homologous end-joining (NHEJ) mechanism to repair the break (Fig. 1a). gRNAs are introduced to cells by a plasmid vector, either through transfection https://www.biomedcentral.com/1471-2164/16/846

15.Addgene:CRISPRReferencesandInformationIn collaboration with the labs who have depositedCRISPR plasmids, we've created a series of links and guides to help you use CRISPR in your lab. Learn More Guide to CRISPR technology Addgene Blog Posts How to Design Your gRNA for CRISPR Genome Editing: John Doench from the Broad Institute http://www.addgene.org/crispr/reference/

16.CRISPR/Cas9系统质粒载体列表262210 pnos-Fok1:dCas9-nos Fok1-dCas9 Insect Expression nanos Bullock CRISPRflydesign(unpublished) 62211 pAct-Fok1:dCas9 Fok1-dCas9 Insect Expression act5C Bullock CRISPRflydesign(unpublished) Purify A catalytically inactive Cas9 (dCas9) fused to an epitope tag(s) can be used to purify genhttp://www.biovector.net/product/133373.html

17.CRISPRdirect2016-12-14 CRISPRdirect shows restriction enzyme cutting sites - Sample 2016-09-09 Added 10 species - List 2016-08-30 Added Human Japanese Reference Genome JRGv1. 2016-06-14 Added 10 species - List 2015-10-05 CRISPRdirect supports 200+ species - List of species 2015-01-13 HTTPShttp://crispr.dbcls.jp/

18.OntargetandoffThe crisprDesign (GitHub link) package provides user-friendly functionalities to extract and score those sequences automatically via the addOnTargetScores function.4 On-targeting efficiency scores Predicting on-target cutting efficiency is an extensive area of research, and we try to provide in crisprhttp://bioconductor.org/packages/devel/bioc/vignettes/crisprScore/inst/doc/crisprScore.html

19.ECRISP:DesignofcustomgRNAconstructsBioinformatics methods can be used to find suitable target sites for the DSB in a systematic manner. We developed E-CRISP to design CRISPR constructs and provide the possibility to alter various design parameters systematically. A fast nucleotide indexing approach and the application of a binary intehttps://thenode.biologists.com/e-crisp-design-of-custom-grna-constructs/research/

20.SequencedeterminantsofimprovedCRISPRsgRNAdesigndifferent from that for CRISPR/Cas9 knockout and propose a new model for predicting sgRNA efficiency in CRISPRi/a experiments. These results facilitate the genome-wide design of improved sgRNA for both knockout and CRISPRi/a studies. Footnoteshttp://doi.org/10.1101/gr.191452.115

21.CRISPR其脱靶评分公式与上述 2.1.5 Cas-OFFinder “CRISPR Design” 软件相同,但仅针对植物进行 该软件[30] 仅可评估 sgRNA 的脱靶效应(http:// sgRNA 设计。最大特色是搜寻sgRNA 靶标位点中是 否含限制性内切酶识别序列,以方便采用酶切法检 /cas-offinder/) ,由韩国首尔国立大 测基因组切割效率。 学(Seoul https://max.book118.com/html/2017/0920/134497738.shtm

22.CloudBenchling is a cloud-based platform for biotechnology research and development and the only biology-first platform for scientific data, collaboration, and insights.https://www.benchling.com/

23.CRISPRVisit the old version ofCRISPR-P Reference 1. Yang Lei, Li Lu, Hai-Yang Liu, Sen L, Feng Xing, Ling-Ling Chen*. CRISPR-P: A web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol Plant, 2014, 7(9): 1494-1496.doi: 10.1093/mp/ssu044. http://crispr.hzau.edu.cn/

24.CRISPRCas9mediatedLAG3disruptioninCARWe obtained the first exon sequence ofLAG-3from NCBI and used the CRISPR Design Tool (http://crispr.mit.edu) to design sgRNAs. Oligonucleotides containing T7 promoter and 20 bp targeting sequences were synthesized as forward primer (Supplementary Table S1). T7-sgRNA PCR product was amplifiedhttps://journal.hep.com.cn/fmd/EN/10.1007/s11684-017-0543-6

25.CRISPRGPT:AnLLMAgentforAutomatedDesignofGeneAfter completing design tasks, CRISPR-GPT offers selected protocols based on the interaction history, including CRISPR system selection and delivery methods (See example in Figure 5 General Task 5). Finally, for the validation task, CRISPR-GPT utilizes external APIs, like Primer3, to assist usershttp://arxiv.org/html/2404.18021v1

26.CRISPRGuideRNADesign:MethodsandProtocolsSpringerLinkThis detailed volume focuses on the CRISPR-associated guide RNA and how it can be designed, modified, and validated for a broad repertoire of purposes. Beginning with a section on computational design of target-specific guide RNAs, the book continues by covering chemical modifications to alter guidhttps://www.springer.com/us/book/9781071606865

27.CRISPRHere we describe a web tool called CRISPR-ERA for automated genome wide sgRNA design. CRISPR-ERA can provide different sgRNA searching approaches for genome editing, such as Cas9 nuclease. In addition, CRISPR-ERA also generate sgRNAs for gene activation or repression using our large-scale databashttp://crispr-era.stanford.edu/

28.SureDesign,用于NGSCGHCRISPRFISH的定制设计安捷伦Agilent SureDesign 为 NGS、CGH、CRISPR 和 FISH 创建定制设计。对于 NGS,SureDesign 支持定制 SureSelect 和 HaloPlex 靶向序列捕获文库设计。对于 CGH,SureDesign 支持用于 CGH、ChIP-on-chip 和 DNA 甲基化的定制微阵列芯片设计。https://www.agilent.com/zh-cn/product/next-generation-sequencing/ngs-data-analysis-interpretation/suredesign-4301564

29.CRISPR/Cas9植物基因敲除试剂盒CRISPR Design:http://cbi.hzau.edu.cn/cgi-bin/CRISPR (2)选取 atttttcagGCTCTACCTAACCAGCAAACCGTAGATTATCCCAGCTTCAAGCTTGTCATTGTTGGTGATGGAGGCACAGgtacggt (3)输入序列信息(以拟南AtRAN1基因为例) (4)点submit,出现右侧结果; (5)根据左边不同Guide序列score的高低选取合适的Guide序列,score的高低并不代表敲https://www.biomart.cn/infosupply/31603201.htm

30.FrontiersCRISPRGeneTherapy:Applications,Limitations(31,57), CRISPR-design, CasOFFinder, and others (31). However, many of these tools are designed based on computational algorithms with varying parameters or rely on phenotypic screens that may be specific to cell types and genomes, generating appreciable noise and lack of generalizability acrosshttps://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2020.01387/full

31.anaccuratecelllineageusingCRISPRrecorders?eLifeComputer simulations reveal the potential and limitations of recently proposed CRISPR-based cell lineage recorders, and suggest how the recorders' design can be optimised to yield more accurate cell lineage trees.http://elifesciences.org/articles/40292