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Predicting subcellular location of apoptosis proteins based on wavelet transform and support vector machine

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Abstract

Apoptosis proteins have a central role in the development and homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. As a result of genome and other sequencing projects, the gap between the number of known apoptosis protein sequences and the number of known apoptosis protein structures is widening rapidly. Because of this extremely unbalanced state, it would be worthwhile to develop a fast and reliable method to identify their subcellular locations so as to gain better insight into their biological functions. In view of this, a new method, in which the support vector machine combines with discrete wavelet transform, has been developed to predict the subcellular location of apoptosis proteins. The results obtained by the jackknife test were quite promising, and indicated that the proposed method can remarkably improve the prediction accuracy of subcellular locations, and might also become a useful high-throughput tool in characterizing other attributes of proteins, such as enzyme class, membrane protein type, and nuclear receptor subfamily according to their sequences.

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Acknowledgments

This work was supported by grants from the National Natural Science Foundation of China (20605010, 20865003, 20805023), the Jiangxi Province Natural Science Foundation (2007JZH2644), the Opening Foundation of State Key Laboratory of Chem/Biosensing and Chemometrics of Hunan University (2006022, 2007012).

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Authors and Affiliations

  1. Department of Chemistry, Nanchang University, 330031, Nanchang, People’s Republic of China

    Jian-Ding Qiu, San-Hua Luo, Jian-Hua Huang, Xing-Yu Sun & Ru-Ping Liang

  2. Department of Chemical Engineering, Pingxiang College, 337055, Pingxiang, People’s Republic of China

    Jian-Ding Qiu

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  1. Jian-Ding Qiu
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  2. San-Hua Luo
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  3. Jian-Hua Huang
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Correspondence to Jian-Ding Qiu.

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Qiu, JD., Luo, SH., Huang, JH. et al. Predicting subcellular location of apoptosis proteins based on wavelet transform and support vector machine. Amino Acids 38, 1201–1208 (2010). https://doi.org/10.1007/s00726-009-0331-y

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