BMCBIOINFORMATICS . BIOMEDCENTRAL . COM {}

Matching Content Categories {📚}

• Social Networks
• Education
• Technology & Computing

Content Management System {📝}

What CMS is bmcbioinformatics.biomedcentral.com built with?

Custom-built

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

Traffic Estimate {📈}

What is the average monthly size of bmcbioinformatics.biomedcentral.com audience?

🚀 Good Traffic: 50k - 100k visitors per month


Based on our best estimate, this website will receive around 50,019 visitors per month in the current month.
However, some sources were not loaded, we suggest to reload the page to get complete results.

check SE Ranking
check Ahrefs
check Similarweb
check Ubersuggest
check Semrush

How Does Bmcbioinformatics.biomedcentral.com Make Money? {💸}

Display Ads {🎯}

Direct Advertisers (3)

How Much Does Bmcbioinformatics.biomedcentral.com Make? {💰}

Display Ads {🎯}

$690 per month
Our calculations suggest that Bmcbioinformatics.biomedcentral.com earns between $462 and $1,271 monthly online from display advertisements.

Keywords {🔍}

bmc, cookies, transposon, privacy, orientation, data, page, capable, site, optional, content, personal, parties, policy, information, manage, bioinformatics, insertion, ciss, specific, driving, genes, encoded, strand, pcr, products, primers, article, contact, editing, authors, choice, essential, make, function, advertising, personalisation, usage, analysis, social, media, accepting, consent, processing, including, transfers, european, economic, area, varying,

Topics {✒️}

authors scientific editing privacy choices/manage cookies bmc sb junction fragments european economic area specific ta sites primers i-iv transposon side primers library specific barcode state privacy rights accepting optional cookies splice site acceptor pcr products derived 1471-2105 contact driving genes encoded manage preferences personal data sb transposon data protection optional cookies genes encoded pcr products essential cookies cookies skip driving transcription cookies policy privacy policy privacy statement usage analysis social media varying standards automated tool genomic region transcript disruption sequencing process general enquiries preference centre springer nature content positive strand transposon choices ciss insertion privacy site strand choice make function

Schema {🗺️}

WebPage:
      mainEntity:
         headline:TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data
         description:Next generation sequencing approaches applied to the analyses of transposon insertion junction fragments generated in high throughput forward genetic screens has created the need for clear informatics and statistical approaches to deal with the massive amount of data currently being generated. Previous approaches utilized to 1) map junction fragments within the genome and 2) identify Common Insertion Sites (CISs) within the genome are not practical due to the volume of data generated by current sequencing technologies. Previous approaches applied to this problem also required significant manual annotation. We describe Transposon Annotation Poisson Distribution Association Network Connectivity Environment (TAPDANCE) software, which automates the identification of CISs within transposon junction fragment insertion data. Starting with barcoded sequence data, the software identifies and trims sequences and maps putative genomic sequence to a reference genome using the bowtie short read mapper. Poisson distribution statistics are then applied to assess and rank genomic regions showing significant enrichment for transposon insertion. Novel methods of counting insertions are used to ensure that the results presented have the expected characteristics of informative CISs. A persistent mySQL database is generated and utilized to keep track of sequences, mappings and common insertion sites. Additionally, associations between phenotypes and CISs are also identified using Fisher’s exact test with multiple testing correction. In a case study using previously published data we show that the TAPDANCE software identifies CISs as previously described, prioritizes them based on p-value, allows holistic visualization of the data within genome browser software and identifies relationships present in the structure of the data. The TAPDANCE process is fully automated, performs similarly to previous labor intensive approaches, provides consistent results at a wide range of sequence sampling depth, has the capability of handling extremely large datasets, enables meaningful comparison across datasets and enables large scale meta-analyses of junction fragment data. The TAPDANCE software will greatly enhance our ability to analyze these datasets in order to increase our understanding of the genetic basis of cancers.
         datePublished:2012-06-29T00:00:00Z
         dateModified:2012-06-29T00:00:00Z
         pageStart:1
         pageEnd:12
         license:http://creativecommons.org/licenses/by/2.0
         sameAs:https://doi.org/10.1186/1471-2105-13-154
         keywords:
            Window Size
            Junction Fragment
            Forward Genetic Screen
            Genomic Window
            Flank Genomic Sequence
            Bioinformatics
            Microarrays
            Computational Biology/Bioinformatics
            Computer Appl. in Life Sciences
            Algorithms
         image:
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig1_HTML.jpg
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig2_HTML.jpg
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig3_HTML.jpg
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig4_HTML.jpg
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig5_HTML.jpg
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig6_HTML.jpg
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig7_HTML.jpg
            https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig8_HTML.jpg
         isPartOf:
            name:BMC Bioinformatics
            issn:
               1471-2105
            volumeNumber:13
            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:Aaron L Sarver
               affiliation:
                     name:University of Minnesota
                     address:
                        name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                        type:PostalAddress
                     type:Organization
               email:[email protected]
               type:Person
               name:Jesse Erdman
               affiliation:
                     name:University of Minnesota
                     address:
                        name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Tim Starr
               affiliation:
                     name:University of Minnesota
                     address:
                        name:Obstetrics, Gynecology & Women's Health and Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                        type:PostalAddress
                     type:Organization
               type:Person
               name:David A Largaespada
               affiliation:
                     name:University of Minnesota
                     address:
                        name:Department of Genetics, Cell Biology and Development and Pediatrics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Kevin A T Silverstein
               affiliation:
                     name:University of Minnesota
                     address:
                        name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                        type:PostalAddress
                     type:Organization
               type:Person
         isAccessibleForFree:1
         type:ScholarlyArticle
      context:https://schema.org
ScholarlyArticle:
      headline:TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data
      description:Next generation sequencing approaches applied to the analyses of transposon insertion junction fragments generated in high throughput forward genetic screens has created the need for clear informatics and statistical approaches to deal with the massive amount of data currently being generated. Previous approaches utilized to 1) map junction fragments within the genome and 2) identify Common Insertion Sites (CISs) within the genome are not practical due to the volume of data generated by current sequencing technologies. Previous approaches applied to this problem also required significant manual annotation. We describe Transposon Annotation Poisson Distribution Association Network Connectivity Environment (TAPDANCE) software, which automates the identification of CISs within transposon junction fragment insertion data. Starting with barcoded sequence data, the software identifies and trims sequences and maps putative genomic sequence to a reference genome using the bowtie short read mapper. Poisson distribution statistics are then applied to assess and rank genomic regions showing significant enrichment for transposon insertion. Novel methods of counting insertions are used to ensure that the results presented have the expected characteristics of informative CISs. A persistent mySQL database is generated and utilized to keep track of sequences, mappings and common insertion sites. Additionally, associations between phenotypes and CISs are also identified using Fisher’s exact test with multiple testing correction. In a case study using previously published data we show that the TAPDANCE software identifies CISs as previously described, prioritizes them based on p-value, allows holistic visualization of the data within genome browser software and identifies relationships present in the structure of the data. The TAPDANCE process is fully automated, performs similarly to previous labor intensive approaches, provides consistent results at a wide range of sequence sampling depth, has the capability of handling extremely large datasets, enables meaningful comparison across datasets and enables large scale meta-analyses of junction fragment data. The TAPDANCE software will greatly enhance our ability to analyze these datasets in order to increase our understanding of the genetic basis of cancers.
      datePublished:2012-06-29T00:00:00Z
      dateModified:2012-06-29T00:00:00Z
      pageStart:1
      pageEnd:12
      license:http://creativecommons.org/licenses/by/2.0
      sameAs:https://doi.org/10.1186/1471-2105-13-154
      keywords:
         Window Size
         Junction Fragment
         Forward Genetic Screen
         Genomic Window
         Flank Genomic Sequence
         Bioinformatics
         Microarrays
         Computational Biology/Bioinformatics
         Computer Appl. in Life Sciences
         Algorithms
      image:
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig1_HTML.jpg
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig2_HTML.jpg
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig3_HTML.jpg
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig4_HTML.jpg
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig5_HTML.jpg
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig6_HTML.jpg
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig7_HTML.jpg
         https://media.springernature.com/lw1200/springer-static/image/art%3A10.1186%2F1471-2105-13-154/MediaObjects/12859_2011_Article_5365_Fig8_HTML.jpg
      isPartOf:
         name:BMC Bioinformatics
         issn:
            1471-2105
         volumeNumber:13
         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:Aaron L Sarver
            affiliation:
                  name:University of Minnesota
                  address:
                     name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
            name:Jesse Erdman
            affiliation:
                  name:University of Minnesota
                  address:
                     name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Tim Starr
            affiliation:
                  name:University of Minnesota
                  address:
                     name:Obstetrics, Gynecology & Women's Health and Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:David A Largaespada
            affiliation:
                  name:University of Minnesota
                  address:
                     name:Department of Genetics, Cell Biology and Development and Pediatrics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Kevin A T Silverstein
            affiliation:
                  name:University of Minnesota
                  address:
                     name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
                     type:PostalAddress
                  type:Organization
            type:Person
      isAccessibleForFree:1
["Periodical","PublicationVolume"]:
      name:BMC Bioinformatics
      issn:
         1471-2105
      volumeNumber:13
Organization:
      name:BioMed Central
      logo:
         url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
         type:ImageObject
      name:University of Minnesota
      address:
         name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
         type:PostalAddress
      name:University of Minnesota
      address:
         name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
         type:PostalAddress
      name:University of Minnesota
      address:
         name:Obstetrics, Gynecology & Women's Health and Masonic Cancer Center, University of Minnesota, Minneapolis, USA
         type:PostalAddress
      name:University of Minnesota
      address:
         name:Department of Genetics, Cell Biology and Development and Pediatrics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
         type:PostalAddress
      name:University of Minnesota
      address:
         name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
         type:PostalAddress
ImageObject:
      url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
      name:Aaron L Sarver
      affiliation:
            name:University of Minnesota
            address:
               name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Jesse Erdman
      affiliation:
            name:University of Minnesota
            address:
               name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
               type:PostalAddress
            type:Organization
      name:Tim Starr
      affiliation:
            name:University of Minnesota
            address:
               name:Obstetrics, Gynecology & Women's Health and Masonic Cancer Center, University of Minnesota, Minneapolis, USA
               type:PostalAddress
            type:Organization
      name:David A Largaespada
      affiliation:
            name:University of Minnesota
            address:
               name:Department of Genetics, Cell Biology and Development and Pediatrics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
               type:PostalAddress
            type:Organization
      name:Kevin A T Silverstein
      affiliation:
            name:University of Minnesota
            address:
               name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
               type:PostalAddress
            type:Organization
PostalAddress:
      name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
      name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
      name:Obstetrics, Gynecology & Women's Health and Masonic Cancer Center, University of Minnesota, Minneapolis, USA
      name:Department of Genetics, Cell Biology and Development and Pediatrics Masonic Cancer Center, University of Minnesota, Minneapolis, USA
      name:Biostatistics and Bioinformatics Masonic Cancer Center, University of Minnesota, Minneapolis, USA

Social Networks {👍}(2)

• https://twitter.com/biomedcentral
• https://www.facebook.com/BioMedCentral

External Links {🔗}(21)

• What's the financial gain of https://www.biomedcentral.com/privacy-statement?
• Financial intake of https://www.biomedcentral.com
• How much does https://www.biomedcentral.com/journals pull in monthly?
• How much revenue does https://www.biomedcentral.com/getpublished bring in?
• Find out how much https://www.biomedcentral.com/about earns monthly
• What's the total monthly financial gain of https://www.biomedcentral.com/account?
• Learn how profitable https://submission.nature.com/new-submission/12859/3 is on a monthly basis
• How much does https://blogs.biomedcentral.com/ pull in monthly?
• Profit of https://www.biomedcentral.com/login
• Learn about the earnings of https://authorservices.springernature.com/go/sn/?utm_source=Website&utm_medium=BMC&utm_campaign=SNAS+Referrals+2022&utm_id=ref2022
• What's the revenue for https://www.biomedcentral.com/about/policies?
• What's https://www.biomedcentral.com/accessibility's gross income?
• What are the total earnings of https://www.biomedcentral.com/about/press-centre?
• How much revenue does https://support.biomedcentral.com/support/home produce monthly?
• https://biomedcentral.typeform.com/to/VLXboo income
• https://www.biomedcentral.com/about/jobs's revenue stream
• How much profit does http://www.weibo.com/biomedcentral make?
• How much cash flow does https://www.biomedcentral.com/terms-and-conditions have monthly?
• What's the income generated by https://www.springernature.com/ccpa each month?
• How much income does https://www.biomedcentral.com/cookies have?
• https://www.springernature.com income

Analytics and Tracking {📊}

• Google Tag Manager

Libraries {📚}

• Prism.js