Abstract
In this paper,we constructed a data set of rice proteins with known locations from SWISS-PROT,using the Support Vector Machine to predicte the type of a given rice protein by incorporating sequence information with physics chemistry property of amino acid. Results are assessed through 5-fold cross-validation tests.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Kumar, A., Agarwal, S., Heyman, J.A., Matson, S., Heidtman, M., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R., Liu, Y., et al.: Subcellular localization of the yeast proteome. Genes. Dev. 16, 707–719 (2002)
Reinhardt, A., Hubbard, T.: Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res. 26, 2230–2236 (1998)
Hua, S., Sun, Z.: Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17, 721–728 (2001), http://www.bioinfo.tsinghua.edu.cn/SubLoc/
Emanuelsson, O., Nielson, H., Brunak, S., von Heijne, G.: Predicting subcellular localization of proteins based on their Nterminal amino acid sequence. J. Mol. Biol. 300, 1005–1016 (2000)
Nair, R., Rost, B.: Inferring subcellular localization through automated lexical analysis. Bioinformatics 18, S78–S86 (2002)
Chou, K.C.: Prediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochem. Biophys. Res. Commun. 278, 477–483 (2000a)
Chou, K.C.: Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins Struct. Funct. Genet. 43, 246–255 (2001)
Cai, Y.D., Liu, X.J., Xu, X.B., Chou, K.C.: Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect. J. Cell. Biochem. 84, 343–348 (2002)
Wang, H.C.: Essentials of Sequence Analysis. Press of Military Medical, Beijing (1994) (Ch)
Guruprasad, K., Reddy, B.V., Pandit, M.W.: Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. 4, 155–161 (1990)
Vapnik, V.: Statistical Learning Theory. Wiley-Interscience, New York (1998)
Cortes, C., Vapnik, V.: Support vector networks. Machine Learning 20, 273–293 (1995)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Li, Nn., Niu, Xh., Shi, F., Li, Xy. (2005). Prediction of Protein Subcellular Locations Using Support Vector Machines. In: Wang, L., Chen, K., Ong, Y.S. (eds) Advances in Natural Computation. ICNC 2005. Lecture Notes in Computer Science, vol 3610. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11539087_140
Download citation
DOI: https://doi.org/10.1007/11539087_140
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28323-2
Online ISBN: 978-3-540-31853-8
eBook Packages: Computer ScienceComputer Science (R0)