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A DNA Sequence Corpus for Compression Benchmark

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Practical Applications of Computational Biology and Bioinformatics, 12th International Conference (PACBB2018 2018)

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 803))

Abstract

The progress in sequencing technologies and the increasing availability of DNA sequences from extant and extinct organisms is shaping our knowledge about species origin and development, as well as originating an improvement of the computational methods for storage and analysis purposes. Given the large volume of DNA sequences, computational models that efficiently represent diverse DNA sequences using low computational resources are very welcome. Currently, for benchmarking compression algorithms there is absence of a standard corpus that enables a wide and fair comparison. This should be a corpus that reflects the main domains and kingdoms, without being exaggerated in size and number of sequences. In this paper, we provide such DNA sequence corpus, overviewing its elements and furnishing a comparison of some of the algorithms for DNA sequence compression. The corpus is available at https://tinyurl.com/DNAcorpus.

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Acknowledgments

This work was partially funded by FEDER (Programa Operacional Factores de Competitividade - COMPETE) and by National Funds through the FCT, in the context of the projects UID/CEC/00127/2013 & PTCD/EEI-SII/6608/2014.

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Authors and Affiliations

  1. IEETA/DETI, University of Aveiro, Aveiro, Portugal

    Diogo Pratas & Armando J. Pinho

Authors
  1. Diogo Pratas
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  2. Armando J. Pinho
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Corresponding author

Correspondence to Diogo Pratas .

Editor information

Editors and Affiliations

  1. Escuela Superior de Ingeniería Informática, Universidad de Vigo, Ourense, Spain

    Florentino Fdez-Riverola

  2. Faculty of Computing, Department of Software Engineering, Universiti Teknologi Malaysia, Johor, Malaysia

    Mohd Saberi Mohamad

  3. Department de Informática, Universidade do Minho, Braga, Portugal

    Miguel Rocha

  4. Departamento de Informática y Automática, Facultad de Ciencias, Universidad de Salamanca, Salamanca, Spain

    Juan F. De Paz

  5. Departamento de Sistemas Informáticos, Universidad de Castilla-La Mancha, Albacete, Albacete, Spain

    Pascual González

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Pratas, D., Pinho, A.J. (2019). A DNA Sequence Corpus for Compression Benchmark. In: Fdez-Riverola, F., Mohamad, M., Rocha, M., De Paz, J., González, P. (eds) Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. PACBB2018 2018. Advances in Intelligent Systems and Computing, vol 803. Springer, Cham. https://doi.org/10.1007/978-3-319-98702-6_25

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