Skip to main content

A Multiobjective SFLA-Based Technique for Predicting Motifs in DNA Sequences

  • Conference paper
Computer Aided Systems Theory - EUROCAST 2013 (EUROCAST 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8111))

Included in the following conference series:

Abstract

In recent years design of new evolutionary techniques for addressing optimization problems is being a booming practice. Furthermore, considering that the vast majority of real optimization problems need to simultaneously optimize more than a single objective function (Multiobjective Optimization Problem - MOP); many of these techniques are also adapted to this multiobjective context. In this paper, we present a multiobjective adaptation of one of the last proposed swarm-based evolutionary algorithms, the Shuffle Frog Leaping Algorithm (SFLA), named Multiobjective Shuffle Frog Leaping Algorithm (MO-SFLA). To evaluate the performance of this new multiobjective algorithm, we have applied it to solve an important biological optimization problem, the Motif Discovery Problem (MDP). As we will see, the structure and operation of MO-SFLA makes it suitable for solving the MDP, achieving better results than other multiobjective evolutionary algorithms and making better predictions than other well-known biological tools.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Deb, K., Pratap, A., Agarwal, S., Meyarivan, T.: A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Transactions on Evolutionary Computation 6, 182–197 (2002)

    Article  Google Scholar 

  2. D’haeseleer, P.: What are DNA sequence motifs? Nature Biotechnology 24(4), 423–425 (2006)

    Article  Google Scholar 

  3. Eusuff, M., Lansey, K.: Optimization of water distribution network design using the shuffled frog-leaping algorithm. Journal of Water Resources Planning & Management 129(3), 210–225 (2003)

    Article  Google Scholar 

  4. Fogel, G.B., Porto, V.W., Varga, G., Dow, E.R., Craven, A.M., Powers, D.M., Harlow, H.B., Su, E.W., Onyia, J.E., Su, C.: Evolutionary computation for discovery of composite transcription factor binding sites. Nucleic Acids Research 36(21), e142 (2008)

    Google Scholar 

  5. Fogel, G.B., Weekes, D.G., Varga, G., Dow, E.R., Harlow, H.B., Onyia, J.E., Su, C.: Discovery of sequence motifs related to coexpression of genes using evolutionary computation. Nucleic Acids Research 32(13), 3826–3835 (2004)

    Article  Google Scholar 

  6. González-Álvarez, D.L., Vega-Rodríguez, M.A., Gómez-Pulido, J.A., Sánchez-Pérez, J.M.: Comparing multiobjective swarm intelligence metaheuristics for DNA motif discovery. Engineering Applications of Artificial Intelligence 26(1), 314–326 (2012)

    Article  Google Scholar 

  7. Tompa, M., et al.: Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology 23(1), 137–144 (2005)

    Article  MathSciNet  Google Scholar 

  8. Wingender, E., Dietze, P., Karas, H., Knuppel, R.: TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research 24(1), 238–241 (1996)

    Article  Google Scholar 

  9. Zitzler, E., Laumanns, M., Thiele, L.: SPEA2: Improving the strength pareto evolutionary algorithm. Technical report tik-report 103, Swiss Federal Institute of Technology Zurich, Switzerland (2001)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

González-Álvarez, D.L., Vega-Rodríguez, M.A. (2013). A Multiobjective SFLA-Based Technique for Predicting Motifs in DNA Sequences. In: Moreno-Díaz, R., Pichler, F., Quesada-Arencibia, A. (eds) Computer Aided Systems Theory - EUROCAST 2013. EUROCAST 2013. Lecture Notes in Computer Science, vol 8111. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-53856-8_30

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-53856-8_30

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-53855-1

  • Online ISBN: 978-3-642-53856-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics