Skip to main content

Improving Enzyme Function Classification Performance Based on Score Fusion Method

  • Conference paper
  • First Online:
Hybrid Artificial Intelligent Systems (HAIS 2015)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 9121))

Included in the following conference series:

Abstract

Enzymes are important in our life and it plays a vital role in the most biological processes. Computational classification of the enzyme’s function is necessary to save efforts and time. In this paper, an information fusion-based approach is proposed. The unknown sequence is classified through aligning it with all labelled sequences using local pairwise sequence alignment based on different score matrices. The outputs of all pairwise sequence alignment processes are represented by a set of scores. The scores of alignment processes are combined using simple fusion rules. The results of the fusion-based approach achieved results better than all individual sequence alignment processes.

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 EPUB and 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

References

  1. Tseng, Y.Y., Li, W.H.: Classification of protein functional surfaces using structural characteristics. Proc. Natl. Acad. Sci. 109(4), 1170–1175 (2012)

    Article  MathSciNet  Google Scholar 

  2. Coste, F., Garet, G., Groisillier, A., Nicolas, J., Tonon, T.: Automated enzyme classification by formal concept analysis. In: Glodeanu, C.V., Kaytoue, M., Sacarea, C. (eds.) ICFCA 2014. LNCS (LNAI), vol. 8478, pp. 235–250. Springer, Heidelberg (2014)

    Chapter  Google Scholar 

  3. Kumar, C., Choudhary, A.: A top-down approach to classify enzyme functional classes and sub-classes using random forest. EURASIP J. Bioinform. Syst. Biol. 2012(1), 1–14 (2012)

    Article  MathSciNet  Google Scholar 

  4. Faria, D., Ferreira, A.E., Falcão, A.O.: Enzyme classification with peptide programs: a comparative study. J. BMC Bioinform. 10(1), 1–9 (2009)

    Article  Google Scholar 

  5. Brown, D.P., Krishnamurthy, N., Sjölander, K.: Automated protein subfamily identification and classification. PLoS Comput. Biol. 3(8), e160 (2007)

    Article  Google Scholar 

  6. Busk, P.K., Lange, L.: Function-based classification of carbohydrate-active enzymes by recognition of short, conserved peptide motifs. Appl. Environ. Microbiol. 79(11), 3380–3391 (2013)

    Article  Google Scholar 

  7. Clark, W.T., Radivojac, P.: Analysis of protein function and its prediction from amino acid sequence. Proteins: Struct. Funct. Bioinform. 79(7), 2086–2096 (2011)

    Article  Google Scholar 

  8. des Jardins, M., Karp, P.D., Krummenacker, M., Lee, T.J., Ouzounis, C.A.: Prediction of enzyme classification from protein sequence without the use of sequence similarity. In: Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, vol. 5, pp. 92–99 (1997)

    Google Scholar 

  9. Mohammed, A., Guda, C.: Computational approaches for automated classification of enzyme sequences. J. proteomics Bioinform. 4, 147–152 (2011)

    Article  Google Scholar 

  10. Lee, B.J., Shin, M.S., Oh, Y.J., Oh, H.S., Ryu, K.H.: Identification of protein functions using a machine-learning approach based on sequence-derived properties. Proteome Sci. 7(1), 7–27 (2009)

    Article  Google Scholar 

  11. Sharif, M.M., Thrwat, A., Amin, I.I., Ella, A., Hefeny, H.A.: Enzyme function classification based on sequence alignment. In: Mandal, J.K., Satapathy, S.C., Sanyal, M.K., Sarkar, P.P., Mukhopadhyay, A. (eds.) Information Systems Design and Intelligent Applications. AISC, vol. 340, pp. 409–418. Springer, Heidelberg (2015)

    Chapter  Google Scholar 

  12. Xiong, J.: Essential Bioinformatics, 1st edn. Cambridge University Press, Cambridge (2006)

    Book  Google Scholar 

  13. Olsson, B., Nilsson, P., Gawronska, B., Persson, A., Ziemke, T., Andler, S.F.: An information fusion approach to controlling complexity in bioinformatics research. In: Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts, pp. 299–304. IEEE (2005)

    Google Scholar 

  14. Ibrahim, A., Tharwat, A.: Biometric authenticationmethods based on ear and finger knuckle images. Int. J. Comput. Sci. Issues (IJCSI) 11(3), 134–138 (2014)

    Google Scholar 

  15. Kuncheva, L.I.: Combining Pattern Classifiers: Methods and Algorithms. Wiley, New York (2004)

    Book  Google Scholar 

  16. Jain, A., Nandakumar, K., Ross, A.: Score normalization in multimodal biometric systems. Pattern Recogn. 38(12), 2270–2285 (2005)

    Article  Google Scholar 

  17. Bairoch, A.: The enzyme database in 2000. J. Nucleic Acids Res. 28(1), 304–305 (2000). doi:10.1093/nar/28.1.304. http://www.expasy.ch/enzyme/

    Article  Google Scholar 

  18. Huang, W.L., Chen, H.M., Hwang, S.F., Ho, S.Y.: Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method. BioSystems 90(2), 405–413 (2007)

    Article  Google Scholar 

  19. Qiu, J.D., Huang, J.H., Shi, S.P., Liang, R.P.: Using the concept of chou’s pseudo amino acid composition to predict enzyme family classes: an approach with support vector machine based on discrete wavelet transform. Protein Pept. Lett. 17(6), 715–722 (2010)

    Article  Google Scholar 

  20. Shen, H.B., Chou, K.C.: Ezypred: a top-down approach for predicting enzyme functional classes and subclasses. Biochem. Biophys. Res. Commun. 364(1), 53–59 (2007)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Alaa Tharwat or Mahir M. Sharif .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this paper

Cite this paper

Tharwat, A., Sharif, M.M., Hassanien, A.E., Hefeny, H.A. (2015). Improving Enzyme Function Classification Performance Based on Score Fusion Method. In: Onieva, E., Santos, I., Osaba, E., Quintián, H., Corchado, E. (eds) Hybrid Artificial Intelligent Systems. HAIS 2015. Lecture Notes in Computer Science(), vol 9121. Springer, Cham. https://doi.org/10.1007/978-3-319-19644-2_44

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-19644-2_44

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19643-5

  • Online ISBN: 978-3-319-19644-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics