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Bioinformatics Advance Access originally published online on June 20, 2006
Bioinformatics 2006 22(14):1784-1785; doi:10.1093/bioinformatics/btl180
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TSSub: eukaryotic protein subcellular localization by extracting features from profiles

Jian Guo * and Yuanlie Lin

Laboratory of Statistical Computation & Bioinformatics, Department of Mathematical Sciences, Tsinghua University Beijing 100084, China

*To whom correspondence should be addressed.

Summary: This paper introduces a new subcellular localization system (TSSub) for eukaryotic proteins. This system extracts features from both profiles and amino acid sequences. Four different features are extracted from profiles by four probabilistic neural network (PNN) classifiers, respectively (the amino acid composition from whole profiles; the amino acid composition from the N-terminus of profiles; the dipeptide composition from whole profiles and the amino acid composition from fragments of profiles). In addition, a support vector machine (SVM) classifier is added to implement the residue-couple feature extracted from amino acid sequences. The results from the five classifiers are fused by an additional SVM classifier. The overall accuracies of this TSSub reach 93.0 and 77.4% on Reinhardt and Hubbard's eukaryotic protein dataset and Huang and Li's eukaryotic protein dataset, respectively. The comparison with existing methods results shows TSSub provides better prediction performance than existing methods.

Availability: The web server is available from http://166.111.24.5/webtools/TSSub/index.html

Contact: guojian99{at}tsinghua.org.cn

Supplementary Information: The Supplementary Data can be downloaded from http://166.111.24.5/webtools/TSSub/Supplementary.htm

Received on April 4, 2006; revised on April 4, 2006; accepted on May 4, 2006

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