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Graph algorithms for DNA sequencing – origins, current models and the future

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  • Blazewicz, Jacek
  • Kasprzak, Marta
  • Kierzynka, Michal
  • Frohmberg, Wojciech
  • Swiercz, Aleksandra
  • Wojciechowski, Pawel
  • Zurkowski, Piotr

Abstract

With the ubiquitous presence of next-generation sequencing in modern biological, genetic, pharmaceutical and medical research, not everyone pays attention to the underlying computational methods. Even fewer researchers know what were the origins of the current models for DNA assembly. We present original graph models used in DNA sequencing by hybridization, discuss their properties and connections between them. We also explain how these graph models evolved to adapt to the characteristics of next-generation sequencing. Moreover, we present a practical comparison of state-of-the-art DNA de novo assembly tools representing these transformed models, i.e. overlap and decomposition-based graphs. Even though the competition is tough, some assemblers perform better and certainly large differences may be observed in hardware resources utilization. Finally, we outline the most important trends in the sequencing field, and try to predict their impact on the computational models in the future.

Suggested Citation

  • Blazewicz, Jacek & Kasprzak, Marta & Kierzynka, Michal & Frohmberg, Wojciech & Swiercz, Aleksandra & Wojciechowski, Pawel & Zurkowski, Piotr, 2018. "Graph algorithms for DNA sequencing – origins, current models and the future," European Journal of Operational Research, Elsevier, vol. 264(3), pages 799-812.
    • Handle: RePEc:eee:ejores:v:264:y:2018:i:3:p:799-812
    DOI: 10.1016/j.ejor.2016.06.043
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    References listed on IDEAS

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    1. Jacek Blazewicz & Edmund Burke & Graham Kendall & Wojciech Mruczkiewicz & Ceyda Oguz & Aleksandra Swiercz, 2013. "A hyper-heuristic approach to sequencing by hybridization of DNA sequences," Annals of Operations Research, Springer, vol. 207(1), pages 27-41, August.
    2. Caroline B. Albertin & Oleg Simakov & Therese Mitros & Z. Yan Wang & Judit R. Pungor & Eric Edsinger-Gonzales & Sydney Brenner & Clifton W. Ragsdale & Daniel S. Rokhsar, 2015. "The octopus genome and the evolution of cephalopod neural and morphological novelties," Nature, Nature, vol. 524(7564), pages 220-224, August.
    3. Jacek Blazewicz & Ceyda Oguz & Aleksandra Swiercz & Jan Weglarz, 2006. "DNA Sequencing by Hybridization via Genetic Search," Operations Research, INFORMS, vol. 54(6), pages 1185-1192, December.
    4. Blum, Christian & Lozano, José A. & Davidson, Pinacho, 2015. "Mathematical programming strategies for solving the minimum common string partition problem," European Journal of Operational Research, Elsevier, vol. 242(3), pages 769-777.
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    Cited by:

    1. Aleksandra Swiercz & Wojciech Frohmberg & Michal Kierzynka & Pawel Wojciechowski & Piotr Zurkowski & Jan Badura & Artur Laskowski & Marta Kasprzak & Jacek Blazewicz, 2018. "GRASShopPER—An algorithm for de novo assembly based on GPU alignments," PLOS ONE, Public Library of Science, vol. 13(8), pages 1-23, August.

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