The Protein Journal

, Volume 29, Issue 2, pp 114–119 | Cite as

Prediction of the Types of Membrane Proteins Based on Discrete Wavelet Transform and Support Vector Machines

  • Jian-Ding Qiu
  • Xing-Yu Sun
  • Jian-Hua Huang
  • Ru-Ping Liang


Membrane proteins are crucial for many biological functions and have become attractive targets for both basic research and drug discovery. With the unprecedented increasing of newly found protein sequences in the post-genomic era, it is both time-consuming and expensive to determine the types of newly found membrane proteins solely with traditional experiment, and so it is highly demanded to develop an automatic method for fast and accurately identifying the type of membrane proteins according to their amino acid sequences. In this study, the discrete wavelet transform (DWT) and support vector machine (SVM) have been used for the prediction of the types of membrane proteins. Maximum accuracy has been obtained using SVM with a wavelet function of bior2.4, a decomposition scale j = 4, and Kyte–Doolittle hydrophobicity scales. The results indicate that the proposed method may play an important complementary role to the existing methods in this area.


Membrane proteins Discrete wavelet transform Support vector machine Jackknife test 



Discrete wavelet transform


Support vector machine


Kyte–Doolittle hydrophobicity


Amino acid


Radial basis function


Daubechies of number


Biorthogonal of number


Symlets of number


Dense alignment surface


Artificial nerve network


Hidden Markov models


Pseudo-amino acid composition


HMM based transmembrane (TM)



This work was supported by grants from the National Natural Science Foundation of China (20605010, 20865003, 20805023), the Jiangxi Province Natural Science Foundation (2007JZH2644), and the Opening Foundation of State Key Laboratory of Chem/Biosensing and Chemometrics of Hunan University (2006022).


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Jian-Ding Qiu
    • 1
  • Xing-Yu Sun
    • 1
  • Jian-Hua Huang
    • 1
  • Ru-Ping Liang
    • 1
  1. 1.Department of Chemistry and Institute for Advanced StudyNanchang UniversityNanchangPeople’s Republic of China

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