We are analyzing https://link.springer.com/article/10.1186/s13059-016-1012-2.

Title:
Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR | Genome Biology
Description:
Background The success of the CRISPR/Cas9 genome editing technique depends on the choice of the guide RNA sequence, which is facilitated by various websites. Despite the importance and popularity of these algorithms, it is unclear to which extent their predictions are in agreement with actual measurements. Results We conduct the first independent evaluation of CRISPR/Cas9 predictions. To this end, we collect data from eight SpCas9 off-target studies and compare them with the sites predicted by popular algorithms. We identify problems in one implementation but found that sequence-based off-target predictions are very reliable, identifying most off-targets with mutation rates superior to 0.1 %, while the number of false positives can be largely reduced with a cutoff on the off-target score. We also evaluate on-target efficiency prediction algorithms against available datasets. The correlation between the predictions and the guide activity varied considerably, especially for zebrafish. Together with novel data from our labs, we find that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro. We further demonstrate that the best predictions can significantly reduce the time spent on guide screening. Conclusions To make these guidelines easily accessible to anyone planning a CRISPR genome editing experiment, we built a new website ( http://crispor.org ) that predicts off-targets and helps select and clone efficient guide sequences for more than 120 genomes using different Cas9 proteins and the eight efficiency scoring systems evaluated here.
Website Age:
28 years and 1 months (reg. 1997-05-29).

Matching Content Categories {📚}

Education
TV
Technology & Computing

Content Management System {📝}

What CMS is link.springer.com built with?

Custom-built

No common CMS systems were detected on Link.springer.com, and no known web development framework was identified.

Traffic Estimate {📈}

What is the average monthly size of link.springer.com audience?

🌠 Phenomenal Traffic: 5M - 10M visitors per month

Based on our best estimate, this website will receive around 7,603,724 visitors per month in the current month.

check SE Ranking
check Ahrefs
check Similarweb
check Ubersuggest
check Semrush

How Does Link.springer.com Make Money? {💸}

The income method remains a mystery to us.

Earning money isn't the goal of every website; some are designed to offer support or promote social causes. People have different reasons for creating websites. This might be one such reason. Link.springer.com might be cashing in, but we can't detect the method they're using.

Keywords {🔍}

guide, pubmed, offtarget, score, additional, file, article, guides, offtargets, data, cas, google, scholar, dataset, scores, sequences, genome, table, mismatches, efficiency, specificity, datasets, number, central, crisprcas, cell, studies, website, crispor, cleavage, shown, sequence, crispr, design, study, rna, figure, modification, fig, doench, tested, code, wang, human, assays, cells, assay, sites, zebrafish, frequencies,

Topics {✒️}

crispr/cas-derived rna-guided endonucleases o-nitrophenyl-β-d-galactopyranosid crispr-cas9-mediated gene inactivation crispr-cas9 genome-editing systems net/harijay/fz-score-d1324dab/ protospacer adjacent motif isolated double-strand breaks �u20s/mef/c6-t7 endo” nonfunctional β-galactosidase gene high-throughput gene targeting sylvie schneider-maunoury mary lyon centre jean-baptiste renaud cas9 rna-guided endonucleases jean-paul concordet integrase-defective lentiviral vectors crispr/cas systems silico predictive modeling avenir—anr-ii-inbs-0014 rna-guided cas9 nucleases genotype-specific cancer liabilities grants nih/nhgri 5u41hg002371-15 genome-wide cas9/grna cd1 pseudo-pregnant females jean-baptiste penigault evidence-based recommendations exist crispr-cas9 nucleases revealed article download pdf genome-wide target specificities specific opportunistic pathogen-free crispr-cas nucleases api-key gratefully provided crispr-cas system true positives + false negatives efficient genome editing crispr-cas9 editing crispr/cas9 guide efficiency moreno-mateos scores perform target search parameters receiver-operating characteristic analysis find crispr-induced modifications 23-bp-long guide sequence flexible guide-rna design tw/~cjlin/libsvm/copyright true positives + false positives assay background information highest moreno-mateos score crispr-cas9 targeting extremely gc-rich guides genome-wide profiling

Questions {❓}

4 high enough to reduce the number of guides in practice?

Schema {🗺️}

WebPage:
      mainEntity:
         headline:Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR
         description:The success of the CRISPR/Cas9 genome editing technique depends on the choice of the guide RNA sequence, which is facilitated by various websites. Despite the importance and popularity of these algorithms, it is unclear to which extent their predictions are in agreement with actual measurements. We conduct the first independent evaluation of CRISPR/Cas9 predictions. To this end, we collect data from eight SpCas9 off-target studies and compare them with the sites predicted by popular algorithms. We identify problems in one implementation but found that sequence-based off-target predictions are very reliable, identifying most off-targets with mutation rates superior to 0.1 %, while the number of false positives can be largely reduced with a cutoff on the off-target score. We also evaluate on-target efficiency prediction algorithms against available datasets. The correlation between the predictions and the guide activity varied considerably, especially for zebrafish. Together with novel data from our labs, we find that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro. We further demonstrate that the best predictions can significantly reduce the time spent on guide screening. To make these guidelines easily accessible to anyone planning a CRISPR genome editing experiment, we built a new website ( http://crispor.org ) that predicts off-targets and helps select and clone efficient guide sequences for more than 120 genomes using different Cas9 proteins and the eight efficiency scoring systems evaluated here.
         datePublished:2016-07-05T00:00:00Z
         dateModified:2016-07-05T00:00:00Z
         pageStart:1
         pageEnd:12
         license:http://creativecommons.org/publicdomain/zero/1.0/
         sameAs:https://doi.org/10.1186/s13059-016-1012-2
         keywords:
            Efficiency Score
            Genome Editing
            Specificity Score
            Guide Sequence
            Protospacer Adjacent Motif
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
         image:
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig1_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig2_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig3_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig4_HTML.gif
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig5_HTML.gif
         isPartOf:
            name:Genome Biology
            issn:
               1474-760X
            volumeNumber:17
            type:
               Periodical
               PublicationVolume
         publisher:
            name:BioMed Central
            logo:
               url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
               type:ImageObject
            type:Organization
         author:
               name:Maximilian Haeussler
               url:http://orcid.org/0000-0001-8721-8253
               affiliation:
                     name:University of California
                     address:
                        name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
                        type:PostalAddress
                     type:Organization
               email:[email protected]
               type:Person
               name:Kai Schönig
               affiliation:
                     name:Heidelberg University
                     address:
                        name:Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Hélène Eckert
               affiliation:
                     name:Institut Curie, CNRS UMR3215, INSERM U934
                     address:
                        name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Alexis Eschstruth
               affiliation:
                     name:CNRS UMR 7622, INSERM U1156
                     address:
                        name:CNRS UMR 7622, INSERM U1156, Paris, France
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Joffrey Mianné
               affiliation:
                     name:Mary Lyon Centre, MRC Harwell
                     address:
                        name:Mary Lyon Centre, MRC Harwell, Didcot, UK
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Jean-Baptiste Renaud
               affiliation:
                     name:TEFOR Infrastructure
                     address:
                        name:TEFOR Infrastructure, Gif-sur-Yvette, France
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Sylvie Schneider-Maunoury
               affiliation:
                     name:CNRS UMR 7622, INSERM U1156
                     address:
                        name:CNRS UMR 7622, INSERM U1156, Paris, France
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Alena Shkumatava
               affiliation:
                     name:Institut Curie, CNRS UMR3215, INSERM U934
                     address:
                        name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Lydia Teboul
               affiliation:
                     name:Mary Lyon Centre, MRC Harwell
                     address:
                        name:Mary Lyon Centre, MRC Harwell, Didcot, UK
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Jim Kent
               affiliation:
                     name:University of California
                     address:
                        name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Jean-Stephane Joly
               affiliation:
                     name:TEFOR Infrastructure
                     address:
                        name:TEFOR Infrastructure, Gif-sur-Yvette, France
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Jean-Paul Concordet
               affiliation:
                     name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle
                     address:
                        name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle, Paris, France
                        type:PostalAddress
                     type:Organization
               email:[email protected]
               type:Person
         isAccessibleForFree:1
         type:ScholarlyArticle
      context:https://schema.org
ScholarlyArticle:
      headline:Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR
      description:The success of the CRISPR/Cas9 genome editing technique depends on the choice of the guide RNA sequence, which is facilitated by various websites. Despite the importance and popularity of these algorithms, it is unclear to which extent their predictions are in agreement with actual measurements. We conduct the first independent evaluation of CRISPR/Cas9 predictions. To this end, we collect data from eight SpCas9 off-target studies and compare them with the sites predicted by popular algorithms. We identify problems in one implementation but found that sequence-based off-target predictions are very reliable, identifying most off-targets with mutation rates superior to 0.1 %, while the number of false positives can be largely reduced with a cutoff on the off-target score. We also evaluate on-target efficiency prediction algorithms against available datasets. The correlation between the predictions and the guide activity varied considerably, especially for zebrafish. Together with novel data from our labs, we find that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro. We further demonstrate that the best predictions can significantly reduce the time spent on guide screening. To make these guidelines easily accessible to anyone planning a CRISPR genome editing experiment, we built a new website ( http://crispor.org ) that predicts off-targets and helps select and clone efficient guide sequences for more than 120 genomes using different Cas9 proteins and the eight efficiency scoring systems evaluated here.
      datePublished:2016-07-05T00:00:00Z
      dateModified:2016-07-05T00:00:00Z
      pageStart:1
      pageEnd:12
      license:http://creativecommons.org/publicdomain/zero/1.0/
      sameAs:https://doi.org/10.1186/s13059-016-1012-2
      keywords:
         Efficiency Score
         Genome Editing
         Specificity Score
         Guide Sequence
         Protospacer Adjacent Motif
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
      image:
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig1_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig2_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig3_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig4_HTML.gif
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2Fs13059-016-1012-2/MediaObjects/13059_2016_1012_Fig5_HTML.gif
      isPartOf:
         name:Genome Biology
         issn:
            1474-760X
         volumeNumber:17
         type:
            Periodical
            PublicationVolume
      publisher:
         name:BioMed Central
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Maximilian Haeussler
            url:http://orcid.org/0000-0001-8721-8253
            affiliation:
                  name:University of California
                  address:
                     name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
            name:Kai Schönig
            affiliation:
                  name:Heidelberg University
                  address:
                     name:Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Hélène Eckert
            affiliation:
                  name:Institut Curie, CNRS UMR3215, INSERM U934
                  address:
                     name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Alexis Eschstruth
            affiliation:
                  name:CNRS UMR 7622, INSERM U1156
                  address:
                     name:CNRS UMR 7622, INSERM U1156, Paris, France
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Joffrey Mianné
            affiliation:
                  name:Mary Lyon Centre, MRC Harwell
                  address:
                     name:Mary Lyon Centre, MRC Harwell, Didcot, UK
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Jean-Baptiste Renaud
            affiliation:
                  name:TEFOR Infrastructure
                  address:
                     name:TEFOR Infrastructure, Gif-sur-Yvette, France
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Sylvie Schneider-Maunoury
            affiliation:
                  name:CNRS UMR 7622, INSERM U1156
                  address:
                     name:CNRS UMR 7622, INSERM U1156, Paris, France
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Alena Shkumatava
            affiliation:
                  name:Institut Curie, CNRS UMR3215, INSERM U934
                  address:
                     name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Lydia Teboul
            affiliation:
                  name:Mary Lyon Centre, MRC Harwell
                  address:
                     name:Mary Lyon Centre, MRC Harwell, Didcot, UK
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Jim Kent
            affiliation:
                  name:University of California
                  address:
                     name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Jean-Stephane Joly
            affiliation:
                  name:TEFOR Infrastructure
                  address:
                     name:TEFOR Infrastructure, Gif-sur-Yvette, France
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Jean-Paul Concordet
            affiliation:
                  name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle
                  address:
                     name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle, Paris, France
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
      isAccessibleForFree:1
["Periodical","PublicationVolume"]:
      name:Genome Biology
      issn:
         1474-760X
      volumeNumber:17
Organization:
      name:BioMed Central
      logo:
         url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
         type:ImageObject
      name:University of California
      address:
         name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
         type:PostalAddress
      name:Heidelberg University
      address:
         name:Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
         type:PostalAddress
      name:Institut Curie, CNRS UMR3215, INSERM U934
      address:
         name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
         type:PostalAddress
      name:CNRS UMR 7622, INSERM U1156
      address:
         name:CNRS UMR 7622, INSERM U1156, Paris, France
         type:PostalAddress
      name:Mary Lyon Centre, MRC Harwell
      address:
         name:Mary Lyon Centre, MRC Harwell, Didcot, UK
         type:PostalAddress
      name:TEFOR Infrastructure
      address:
         name:TEFOR Infrastructure, Gif-sur-Yvette, France
         type:PostalAddress
      name:CNRS UMR 7622, INSERM U1156
      address:
         name:CNRS UMR 7622, INSERM U1156, Paris, France
         type:PostalAddress
      name:Institut Curie, CNRS UMR3215, INSERM U934
      address:
         name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
         type:PostalAddress
      name:Mary Lyon Centre, MRC Harwell
      address:
         name:Mary Lyon Centre, MRC Harwell, Didcot, UK
         type:PostalAddress
      name:University of California
      address:
         name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
         type:PostalAddress
      name:TEFOR Infrastructure
      address:
         name:TEFOR Infrastructure, Gif-sur-Yvette, France
         type:PostalAddress
      name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle
      address:
         name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle, Paris, France
         type:PostalAddress
ImageObject:
      url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
      name:Maximilian Haeussler
      url:http://orcid.org/0000-0001-8721-8253
      affiliation:
            name:University of California
            address:
               name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Kai Schönig
      affiliation:
            name:Heidelberg University
            address:
               name:Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
               type:PostalAddress
            type:Organization
      name:Hélène Eckert
      affiliation:
            name:Institut Curie, CNRS UMR3215, INSERM U934
            address:
               name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
               type:PostalAddress
            type:Organization
      name:Alexis Eschstruth
      affiliation:
            name:CNRS UMR 7622, INSERM U1156
            address:
               name:CNRS UMR 7622, INSERM U1156, Paris, France
               type:PostalAddress
            type:Organization
      name:Joffrey Mianné
      affiliation:
            name:Mary Lyon Centre, MRC Harwell
            address:
               name:Mary Lyon Centre, MRC Harwell, Didcot, UK
               type:PostalAddress
            type:Organization
      name:Jean-Baptiste Renaud
      affiliation:
            name:TEFOR Infrastructure
            address:
               name:TEFOR Infrastructure, Gif-sur-Yvette, France
               type:PostalAddress
            type:Organization
      name:Sylvie Schneider-Maunoury
      affiliation:
            name:CNRS UMR 7622, INSERM U1156
            address:
               name:CNRS UMR 7622, INSERM U1156, Paris, France
               type:PostalAddress
            type:Organization
      name:Alena Shkumatava
      affiliation:
            name:Institut Curie, CNRS UMR3215, INSERM U934
            address:
               name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
               type:PostalAddress
            type:Organization
      name:Lydia Teboul
      affiliation:
            name:Mary Lyon Centre, MRC Harwell
            address:
               name:Mary Lyon Centre, MRC Harwell, Didcot, UK
               type:PostalAddress
            type:Organization
      name:Jim Kent
      affiliation:
            name:University of California
            address:
               name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
               type:PostalAddress
            type:Organization
      name:Jean-Stephane Joly
      affiliation:
            name:TEFOR Infrastructure
            address:
               name:TEFOR Infrastructure, Gif-sur-Yvette, France
               type:PostalAddress
            type:Organization
      name:Jean-Paul Concordet
      affiliation:
            name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle
            address:
               name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle, Paris, France
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
      name:Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
      name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
      name:CNRS UMR 7622, INSERM U1156, Paris, France
      name:Mary Lyon Centre, MRC Harwell, Didcot, UK
      name:TEFOR Infrastructure, Gif-sur-Yvette, France
      name:CNRS UMR 7622, INSERM U1156, Paris, France
      name:Institut Curie, CNRS UMR3215, INSERM U934, Paris, France
      name:Mary Lyon Centre, MRC Harwell, Didcot, UK
      name:Santa Cruz Genomics Institute, MS CBSE, University of California, Santa Cruz, USA
      name:TEFOR Infrastructure, Gif-sur-Yvette, France
      name:INSERM U1154, CNRS UMR 7196, Muséum National d’Histoire Naturelle, Paris, France

External Links {🔗}(269)

Analytics and Tracking {📊}

Google Tag Manager

Libraries {📚}

Clipboard.js
Prism.js

CDN Services {📦}

Crossref

5s.

LINK . SPRINGER . COM {}