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LINK . SPRINGER . COM {}

  1. Analyzed Page
  2. Matching Content Categories
  3. CMS
  4. Monthly Traffic Estimate
  5. How Does Link.springer.com Make Money
  6. Keywords
  7. Topics
  8. Schema
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  10. Analytics And Tracking
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We are analyzing https://link.springer.com/article/10.1186/1471-2105-9-431.

Title:
Probabilistic base calling of Solexa sequencing data | BMC Bioinformatics
Description:
Background Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. Results We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. Conclusion We show that the method improves genome coverage and number of usable tags as compared with Solexa
Website Age:
28 years and 1 months (reg. 1997-05-29).

Matching Content Categories {📚}

  • Video & Online Content
  • Telecommunications
  • Education

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 8,170,536 visitors per month in the current month.

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

We see no obvious way the site makes money.

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 has a revenue plan, but it's either invisible or we haven't found it.

Keywords {🔍}

sequencing, base, tags, data, genome, article, pubmed, rolexa, google, scholar, calling, solexa, bases, figure, quality, file, analysis, number, sequence, dna, coverage, intensity, cycle, iupac, intensities, length, channels, cas, image, cutoffs, tag, central, information, reference, score, colony, entropy, function, access, probability, performed, fastq, mapping, authors, research, bioinformatics, full, match, average, files,

Topics {✒}

high-throughput dna sequencing double-stranded genomic adapters open access article single-stranded dna virus high-throughput data poses solexa/illumina sequencer generates article download pdf high-performance computing facility perform paired-end sequencing high-throughput sequencing information-theoretic base calling enhanced model-based clustering high-throughput techniques high resolution access probabilistic base calling information based metrics construct position-weight matrices long-range pcr amplification[30] full size image designed quality metrics model-based clustering algorithm model-based clustering algorithm[12 dna double helix model-based cluster analysis illumina cluster station arabidopsis methylation patterns[12] illumina software suite sequencing genomic dna paired-end sequencing estimate error rates felix naef high-resolution profiling solexa read mapping dye-specific chemical effects privacy choices/manage cookies error rate defined increased throughput requires short reads assembled common dna variation solexa base calling solexa base-calling large file size probable base calling related subjects de-novo sequencing[9 de-novo sequencing base-pairing contributions authors’ original file protein-dna interactions[7 t4 dna polymerase

Schema {đŸ—ș}

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         headline:Probabilistic base calling of Solexa sequencing data
         description:Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.
         datePublished:2008-10-13T00:00:00Z
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            Solexa Sequence
            Estimate Error Rate
            Probability Simplex
            IUPAC Code
            Bioinformatics
            Microarrays
            Computational Biology/Bioinformatics
            Computer Appl. in Life Sciences
            Algorithms
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      headline:Probabilistic base calling of Solexa sequencing data
      description:Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.
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      dateModified:2008-10-13T00:00:00Z
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         Solexa Sequence
         Estimate Error Rate
         Probability Simplex
         IUPAC Code
         Bioinformatics
         Microarrays
         Computational Biology/Bioinformatics
         Computer Appl. in Life Sciences
         Algorithms
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                     name:School of Life Sciences, Ecole Polytechnique FĂ©dĂ©rale de Lausanne (EPFL), Lausanne, Switzerland
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                     name:School of Life Sciences, Ecole Polytechnique FĂ©dĂ©rale de Lausanne (EPFL), Lausanne, Switzerland
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                  address:
                     name:Fasteris SA, Plan-les-Ouates, Switzerland
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Ioannis Xenarios
            affiliation:
                  name:UniversitĂ© de Lausanne
                  address:
                     name:Swiss Institute of Bioinformatics (SIB), BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
                     type:PostalAddress
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                  name:UniversitĂ© de Lausanne
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                     name:Vital-IT, BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
                     type:PostalAddress
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      affiliation:
            name:Fasteris SA
            address:
               name:Fasteris SA, Plan-les-Ouates, Switzerland
               type:PostalAddress
            type:Organization
      name:Ioannis Xenarios
      affiliation:
            name:UniversitĂ© de Lausanne
            address:
               name:Swiss Institute of Bioinformatics (SIB), BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
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            name:UniversitĂ© de Lausanne
            address:
               name:Vital-IT, BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
               type:PostalAddress
            type:Organization
      name:Felix Naef
      affiliation:
            name:School of Life Sciences, Ecole Polytechnique FĂ©dĂ©rale de Lausanne (EPFL)
            address:
               name:School of Life Sciences, Ecole Polytechnique FĂ©dĂ©rale de Lausanne (EPFL), Lausanne, Switzerland
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      name:School of Life Sciences, Ecole Polytechnique FĂ©dĂ©rale de Lausanne (EPFL), Lausanne, Switzerland
      name:Swiss Institute of Bioinformatics (SIB), BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
      name:School of Life Sciences, Ecole Polytechnique FĂ©dĂ©rale de Lausanne (EPFL), Lausanne, Switzerland
      name:Swiss Institute of Bioinformatics (SIB), BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
      name:Ludwig Institute for Cancer Research (LICR), BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
      name:Swiss Institute of Bioinformatics (SIB), BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
      name:Fasteris SA, Plan-les-Ouates, Switzerland
      name:Swiss Institute of Bioinformatics (SIB), BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
      name:Vital-IT, BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland
      name:School of Life Sciences, Ecole Polytechnique FĂ©dĂ©rale de Lausanne (EPFL), Lausanne, Switzerland
      name:Swiss Institute of Bioinformatics (SIB), BĂątiment GĂ©nopode, UniversitĂ© de Lausanne, Lausanne, Switzerland

External Links {🔗}(125)

Analytics and Tracking {📊}

  • Google Tag Manager

Libraries {📚}

  • Clipboard.js
  • Prism.js

CDN Services {📩}

  • Crossref

4.67s.