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6th International Conference on Practical Applications of Computational Biology & Bioinformatics pp 231–239Cite as

Compact Representation of Biological Sequences Using Set Decision Diagrams

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

Abstract

Nowadays, the exponential availability of biological sequences and the complexity of the computational methods that use them as input motivate the research of new compact representations. To this end, we propose an alternative method for storing sets of sequences based on set decision diagrams instead of classical compression techniques. The set decision diagrams are an extension of the reduced ordered binary decision diagrams, a graph data structure used as a symbolic compact representation of sets or relations between sets. Some experiments with genes of the mitochondrion DNA support the feasibility of our approach.

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Authors and Affiliations

  1. Department of Computer Science and Systems Engineering (DIIS)/, Aragon Institute of Engineering Research (I3A), Universidad de Zaragoza, C/ María de Luna 1, 50018, Zaragoza, Spain

    José Ignacio Requeno & José Manuel Colom

Authors
  1. José Ignacio Requeno
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  2. José Manuel Colom
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Corresponding author

Correspondence to José Ignacio Requeno .

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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Requeno, J.I., Colom, J.M. (2012). Compact Representation of Biological Sequences Using Set Decision Diagrams. 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_27

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  • DOI: https://doi.org/10.1007/978-3-642-28839-5_27

  • 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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