We are analyzing https://link.springer.com/article/10.1186/s13059-015-0784-0.

Title:
WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system | Genome Biology
Description:
The CRISPR/Cas9 system has been rapidly adopted for genome editing. However, one major issue with this system is the lack of robust bioinformatics tools for design of single guide RNA (sgRNA), which determines the efficacy and specificity of genome editing. To address this pressing need, we analyze CRISPR RNA-seq data and identify many novel features that are characteristic of highly potent sgRNAs. These features are used to develop a bioinformatics tool for genome-wide design of sgRNAs with improved efficiency. These sgRNAs as well as the design tool are freely accessible via a web server, WU-CRISPR ( http://crispr.wustl.edu ).
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Keywords {🔍}

pubmed, sequence, cas, article, sgrnas, functional, genome, sgrna, google, scholar, guide, design, crispr, crisprcas, editing, grna, grnas, rna, features, central, analysis, nonfunctional, data, wucrispr, structural, study, system, target, activities, specificity, experimental, structure, end, svm, model, compared, nucleotides, fig, nat, rnas, significant, crossvalidation, chari, sequences, algorithm, prediction, accessibility, positions, bioinformatics, efficacy,

Topics {✒️}

support vector machine org/rnai/public/analysis-tools/sgrna-design weijun liu & xiaowei wang crispr-cas9-mediated gene inactivation crispr-cas9 genome-editing systems position-specific nucleotide accessibilities rna-programmed genome editing extended stem-loop structure position-specific nucleotide accessibility trans-encoded small rna stable rna/dna duplexes small-scale genomic alterations rna-guided cas9 nucleases rna-guided crispr cas9 cas9-based genome editing crispr/cas systems article download pdf natural crispr/cas9 process natural crispr/cas9 system cas protein complex gene-based cross-validation crispr-cas nucleases supplementary tables s1–s3 crispr-cas system pam-proximal seed region functional rna–protein complex tsai sq providing cross-validation data free energy calculation tenfold cross-validation results horizontal gene transfer pre-screened training data trans-activating crrna adaptive bacterial immunity related subjects genome-wide profiling ncbi gene ids crispr endonuclease cas9 grna/target sequence duplex full access precision-recall curve analysis privacy choices/manage cookies long noncoding rnas sequence motifs related short repeats interspaced creative commons license crispr-encoded rnas article wong inefficient genome editing efficient genome editing

Schema {🗺️}

WebPage:
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         headline:WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system
         description:The CRISPR/Cas9 system has been rapidly adopted for genome editing. However, one major issue with this system is the lack of robust bioinformatics tools for design of single guide RNA (sgRNA), which determines the efficacy and specificity of genome editing. To address this pressing need, we analyze CRISPR RNA-seq data and identify many novel features that are characteristic of highly potent sgRNAs. These features are used to develop a bioinformatics tool for genome-wide design of sgRNAs with improved efficiency. These sgRNAs as well as the design tool are freely accessible via a web server, WU-CRISPR ( http://crispr.wustl.edu ).
         datePublished:2015-11-02T00:00:00Z
         dateModified:2015-11-02T00:00:00Z
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         keywords:
            Support Vector Machine
            Support Vector Machine Model
            Seed Region
            Genome Editing
            Guide Sequence
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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ScholarlyArticle:
      headline:WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system
      description:The CRISPR/Cas9 system has been rapidly adopted for genome editing. However, one major issue with this system is the lack of robust bioinformatics tools for design of single guide RNA (sgRNA), which determines the efficacy and specificity of genome editing. To address this pressing need, we analyze CRISPR RNA-seq data and identify many novel features that are characteristic of highly potent sgRNAs. These features are used to develop a bioinformatics tool for genome-wide design of sgRNAs with improved efficiency. These sgRNAs as well as the design tool are freely accessible via a web server, WU-CRISPR ( http://crispr.wustl.edu ).
      datePublished:2015-11-02T00:00:00Z
      dateModified:2015-11-02T00:00:00Z
      pageStart:1
      pageEnd:8
      license:http://creativecommons.org/publicdomain/zero/1.0/
      sameAs:https://doi.org/10.1186/s13059-015-0784-0
      keywords:
         Support Vector Machine
         Support Vector Machine Model
         Seed Region
         Genome Editing
         Guide Sequence
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-015-0784-0/MediaObjects/13059_2015_784_Fig3_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-015-0784-0/MediaObjects/13059_2015_784_Fig4_HTML.gif
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            name:Weijun Liu
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               type:PostalAddress
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            address:
               name:Department of Radiation Oncology, Washington University School of Medicine, St Louis, USA
               type:PostalAddress
            type:Organization
      name:Weijun Liu
      affiliation:
            name:Washington University School of Medicine
            address:
               name:Department of Radiation Oncology, Washington University School of Medicine, St Louis, USA
               type:PostalAddress
            type:Organization
      name:Xiaowei Wang
      affiliation:
            name:Washington University School of Medicine
            address:
               name:Department of Radiation Oncology, Washington University School of Medicine, St Louis, USA
               type:PostalAddress
            type:Organization
            name:Washington University
            address:
               name:Department of Biomedical Engineering, Washington University, St Louis, USA
               type:PostalAddress
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PostalAddress:
      name:Department of Biomedical Engineering, Washington University, St Louis, USA
      name:Department of Radiation Oncology, Washington University School of Medicine, St Louis, USA
      name:Department of Radiation Oncology, Washington University School of Medicine, St Louis, USA
      name:Department of Radiation Oncology, Washington University School of Medicine, St Louis, USA
      name:Department of Biomedical Engineering, Washington University, St Louis, USA

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