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Information Sciences and Systems 2015 pp 307–317Cite as

Proposal of a New Method for de Novo DNA Sequence Assembly Using de Bruijn Graphs

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Part of the book series: Lecture Notes in Electrical Engineering ((LNEE,volume 363))

Abstract

In this work, we propose a method where all main concerns in the construction of a DNA sequence assembler is encompassed in a single computational approach. The graph that represents sequences and their relationships is broken into simpler components through a matching approach on bipartite graphs, which we show to be very suitable for parallelism. Next, a simple heuristic is used to combine the components into long paths in the graph, which correspond to contigs in the genome. Experiments with five datasets have shown high quality assemblies.

Couto and Cerqueira contributed equally to this work.

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Notes

  1. 1.

    http://www.ebi.ac.uk/goldman-srv/simNGS/simNGS/man/simLibrary.1.html.

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Acknowledgments

This work is supported by FAPEMIG, CAPES, and CNPq.

Author information

Authors and Affiliations

  1. Department of Informatics, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil

    Adriano Donato Couto, Fabio Ribeiro Cerqueira, Ricardo dos Santos Ferreira & Alcione de Paiva Oliveira

Authors
  1. Adriano Donato Couto
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  2. Fabio Ribeiro Cerqueira
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  3. Ricardo dos Santos Ferreira
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  4. Alcione de Paiva Oliveira
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Corresponding author

Correspondence to Fabio Ribeiro Cerqueira .

Editor information

Editors and Affiliations

  1. Department of Electrical, Imperial College, London, United Kingdom

    Omer H. Abdelrahman

  2. Department of Electrical and Electronic Engineering, Imperial College, London, United Kingdom

    Erol Gelenbe

  3. Department of Electrical and Electronic Engineering, Imperial College, London, United Kingdom

    Gokce Gorbil

  4. Department of Engineering Technology, University of Houston, Houston, Texas, USA

    Ricardo Lent

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© 2016 Springer International Publishing Switzerland

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Couto, A.D., Cerqueira, F.R., dos Santos Ferreira, R., de Paiva Oliveira, A. (2016). Proposal of a New Method for de Novo DNA Sequence Assembly Using de Bruijn Graphs. In: Abdelrahman, O., Gelenbe, E., Gorbil, G., Lent, R. (eds) Information Sciences and Systems 2015. Lecture Notes in Electrical Engineering, vol 363. Springer, Cham. https://doi.org/10.1007/978-3-319-22635-4_28

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  • DOI: https://doi.org/10.1007/978-3-319-22635-4_28

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-22634-7

  • Online ISBN: 978-3-319-22635-4

  • eBook Packages: EngineeringEngineering (R0)

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