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A Multi-objective Optimization Framework for Multiple Sequence Alignment with Metaheuristics

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Bioinformatics and Biomedical Engineering (IWBBIO 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10209))

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Abstract

The alignment of more than two biological sequences is a widely used technique in a number of areas of computational biology. However, finding an optimal alignment has been shown to be an NP-complete optimization problem. Furthermore, Multiple Sequence Alignment (MSA) can be formulated according to more than one score function, leading to multi-objective formulations of this problem. Due to these reasons, metaheuristics have been proposed to deal with MSA problems. In this paper, we present jMetalMSA, an Open Source software tool for solving MSA problems with multi-objective metaheuristics. Our motivation here is to offer to the scientific community in computational biology, a platform including state-of-the-art optimization algorithms aimed at solving different formulations of the MSA. We describe the main features of jMetalMSA, including the metaheuristics and scores that are currently available. In addition, we show a working example for illustration purposes.

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Notes

  1. 1.

    jMetalMSA project in GitHub: http://github.com/jmetal/jmetalmsa.

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Acknowledgements

This work has been partially supported by the Secretaría Nacional de Educación Superior Ciencia y Tecnología SENESCYT from Ecuador, and Spanish Grants TIN2014-58304-R (Ministerio de Economía y Competitividad), P11-TIC-7529 and P12-TIC-1519 (Plan Andaluz I+D+I - Junta de Andalucía). José García-Nieto is recipient of a Post-Doctoral fellowship of “Captación de Talento para la Investigación” at Universidad de Málaga.

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Authors and Affiliations

  1. Facultad de Ciencias de la Ingeniería, Universidad Técnica Estatal de Quevedo, Quevedo, Los Ríos, Ecuador

    Cristian Zambrano-Vega

  2. Edificio de Investigación Ada Byron, University of Málaga, Málaga, Spain

    Antonio J. Nebro, José García-Nieto & José F. Aldana-Montes

Authors
  1. Cristian Zambrano-Vega
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  2. Antonio J. Nebro
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  3. José García-Nieto
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  4. José F. Aldana-Montes
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Corresponding author

Correspondence to Antonio J. Nebro .

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Editors and Affiliations

  1. Universidad de Granada, Granada, Spain

    Ignacio Rojas

  2. Universidad de Granada, Granada, Spain

    Francisco Ortuño

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Zambrano-Vega, C., Nebro, A.J., García-Nieto, J., Aldana-Montes, J.F. (2017). A Multi-objective Optimization Framework for Multiple Sequence Alignment with Metaheuristics. In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2017. Lecture Notes in Computer Science(), vol 10209. Springer, Cham. https://doi.org/10.1007/978-3-319-56154-7_23

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  • DOI: https://doi.org/10.1007/978-3-319-56154-7_23

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  • Publisher Name: Springer, Cham

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  • Online ISBN: 978-3-319-56154-7

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