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Highly Parallel Convolution Method to Compare DNA Sequences with Enforced In/Del and Mutation Tolerance

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Bioinformatics and Biomedical Engineering (IWBBIO 2020)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 12108))

Abstract

New error tolerant method for the comparison and analysis of symbol sequences is proposed. The method is based on convolution function calculation, where the function is defined over the binary numeric sequences obtained by the specific transformation of original symbol sequence. The method allows highly parallel implementation and is of great value for insertion/delition mutations search. To calculate the convolution function, fast Fourier transform is used in the method implementation.

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Notes

  1. 1.

    Actually, there is no difference between insertion and deletion: changing a reference sequence, one always is able to convert the situation to a single mutation, e. g. to insertion.

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Author information

Authors and Affiliations

  1. Institute of computational modelling of SB RAS, Akademgorodok, 660036, Krasnoyarsk, Russia

    Vladimir Shaidurov, Eugenia Karepova & Michael Sadovsky

  2. Tianjin University of Finance and Economics, Zhujiang Road, 25, Tianjin, 300222, China

    Vladimir Shaidurov

  3. Siberian federal university, Svobodny prosp., 79, Krasnoyarsk, 660041, Russia

    Anna Molyavko, Eugenia Karepova & Michael Sadovsky

Authors
  1. Anna Molyavko
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  2. Vladimir Shaidurov
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  3. Eugenia Karepova
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  4. Michael Sadovsky
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Corresponding author

Correspondence to Michael Sadovsky .

Editor information

Editors and Affiliations

  1. University of Granada, Granada, Spain

    Ignacio Rojas

  2. University of Granada, Granada, Spain

    Olga Valenzuela

  3. University of Granada, Granada, Spain

    Fernando Rojas

  4. University of Granada, Granada, Spain

    Luis Javier Herrera

  5. University of Chicago and Fundacion Progreso y Salud, Granada, Spain

    Francisco Ortuño

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Molyavko, A., Shaidurov, V., Karepova, E., Sadovsky, M. (2020). Highly Parallel Convolution Method to Compare DNA Sequences with Enforced In/Del and Mutation Tolerance. In: Rojas, I., Valenzuela, O., Rojas, F., Herrera, L., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2020. Lecture Notes in Computer Science(), vol 12108. Springer, Cham. https://doi.org/10.1007/978-3-030-45385-5_42

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  • DOI: https://doi.org/10.1007/978-3-030-45385-5_42

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-45384-8

  • Online ISBN: 978-3-030-45385-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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