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PHYSER: An Algorithm to Detect Sequencing Errors from Phylogenetic Information

  • Conference paper
6th International Conference on Practical Applications of Computational Biology & Bioinformatics

Part of the book series: Advances in Intelligent and Soft Computing ((AINSC,volume 154))

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Abstract

Sequencing errors can be difficult to detect due to the high rate of production of new data, which makes manual curation unfeasible. To address these shortcomings we have developed a phylogenetic inspired algorithm to assess the quality of new sequences given a related phylogeny. Its performance and efficiency have been evaluated with human mitochondrial DNA data.

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Author information

Authors and Affiliations

  1. Dept. de Informática e Ingeniería de Sistemas (DIIS) & Instituto de Investigación en Ingeniería de Aragón (I3A), Universidad de Zaragoza, María de Luna 1, 50018, Zaragoza, Spain

    Jorge Álvarez-Jarreta & Elvira Mayordomo

  2. Centro de Invest. Biomédica en Red de Enfermedades Raras & Agencia Aragonesa para la Investigación y el Desarrollo & Dept. de Bioquímica y Biología Molecular y Celular, Facultad de Veterinaria, Universidad de Zaragoza, Miguel Servet 177, 50013, Zaragoza, Spain

    Eduardo Ruiz-Pesini

Authors
  1. Jorge Álvarez-Jarreta
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  2. Elvira Mayordomo
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  3. Eduardo Ruiz-Pesini
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Corresponding author

Correspondence to Jorge Álvarez-Jarreta .

Editor information

Editors and Affiliations

  1. , Dep. Informática / CCTC, Universidade do Minho, Largo do Paco, Braga, 4710 - 057, Portugal

    Miguel P. Rocha

  2. European Bioinformatics Institute, Wellcome Trust Genome Campus, EMBL Outstation - Hinxton, Hinxton, CB10 1SD, United Kingdom

    Nicholas Luscombe

  3. , Department of Informatics, University of Vigo, Edificio Politécnico. Campus Universitario As Lagoas s/n, Ourense, 32004, Spain

    Florentino Fdez-Riverola

  4. Faculty of Science, Department of Computing Science, University of Salamanca, Plaza de la Merced S/N, Salamanca, 37008, Spain

    Juan M. Corchado Rodríguez

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© 2012 Springer-Verlag Berlin Heidelberg

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Álvarez-Jarreta, J., Mayordomo, E., Ruiz-Pesini, E. (2012). PHYSER: An Algorithm to Detect Sequencing Errors from Phylogenetic Information. In: Rocha, M., Luscombe, N., Fdez-Riverola, F., Rodríguez, J. (eds) 6th International Conference on Practical Applications of Computational Biology & Bioinformatics. Advances in Intelligent and Soft Computing, vol 154. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28839-5_12

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  • DOI: https://doi.org/10.1007/978-3-642-28839-5_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-28838-8

  • Online ISBN: 978-3-642-28839-5

  • eBook Packages: EngineeringEngineering (R0)

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