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Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes

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Practical Applications of Computational Biology and Bioinformatics, 13th International Conference (PACBB 2019)

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 1005 ))

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Abstract

Primer and adapter sequences are synthetic DNA or RNA oligonucleotides used in the process of amplification and sequencing. In theory, while similar primer sequences can be present on assembled genomes, adapter sequences should be trimmed (filtered) and, hence, absent from assembled genomes. However, given ambiguity problems, inefficient parameterization of trimming tools, and others, uncommonly they can be found in assembled genomes, on an exact or approximate state. In this paper, we investigate the occurrence of exact and approximate primer-adapter subsequences in assembled and, specifically, in the whole archaeal genomes of the NCBI database. We present a new method that combines data compression with custom signal processing operations, namely filtering and segmentation, to localize and visualize these regions given a defined similarity threshold. The program is freely available, under GPLv3 license, at https://github.com/pratas/maple.

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Acknowledgements

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/00127/2019 & PTCD/EEI-SII/6608/2014 and the grant PD/BD/113969/2015 to MH.

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Authors and Affiliations

  1. IEETA, University of Aveiro, Aveiro, Portugal

    Diogo Pratas, Morteza Hosseini & Armando J. Pinho

  2. DETI, University of Aveiro, Aveiro, Portugal

    Armando J. Pinho

Authors
  1. Diogo Pratas
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  2. Morteza Hosseini
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  3. Armando J. Pinho
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Corresponding author

Correspondence to Diogo Pratas .

Editor information

Editors and Affiliations

  1. Edificio Politécnico, Escuela Superior de Ingeniería Informática,Campus Universitario As Lagoas , Ourense, Spain

    Florentino Fdez-Riverola

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

    Miguel Rocha

  3. Faculty of Bioengineering and Technology, Universiti Malaysia Kelantan, Kelantan, Malaysia

    Mohd Saberi Mohamad

  4. Department of Computer Science and Software Engineering Leader, Data Science Research Group, College of Information Technology (CIT) United Arab Emirates University (UAEU), Al Ain, United Arab Emirates

    Nazar Zaki

  5. IBSAL/BISITE Research Group, University of Salamanca, Salamanca, Salamanca, Spain

    José A. Castellanos-Garzón

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Pratas, D., Hosseini, M., Pinho, A.J. (2020). Visualization of Similar Primer and Adapter Sequences in Assembled Archaeal Genomes. In: Fdez-Riverola, F., Rocha, M., Mohamad, M., Zaki, N., Castellanos-Garzón, J. (eds) Practical Applications of Computational Biology and Bioinformatics, 13th International Conference. PACBB 2019. Advances in Intelligent Systems and Computing, vol 1005 . Springer, Cham. https://doi.org/10.1007/978-3-030-23873-5_16

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