A comparative study on feature extraction from protein sequences for subcellular localization prediction

Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06

Volumn , Issue , 2006, Pages 201-208

  Yang, Wen Yun ^a   Lu, Bao Liang ^a,b   Yang, Yang ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b Shanghai Jiao Tong University   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINATION; AMINES; AMINO ACIDS; ARTIFICIAL INTELLIGENCE; BIOCOMMUNICATIONS; BIOINFORMATICS; BIOLOGY; DATABASE SYSTEMS; DECISION SUPPORT SYSTEMS; EXPERIMENTS; FORECASTING; IMAGE SEGMENTATION; INFORMATION MANAGEMENT; INFORMATION SCIENCE; INTELLIGENT CONTROL; MULTILAYER NEURAL NETWORKS; ORGANIC ACIDS; SEARCH ENGINES; SUPPORT VECTOR MACHINES;

AMINO ACID COMPOSITIONS; AMINO-ACID SEQUENCES; CENTRAL PROBLEMS; CHARACTERISTIC REPRESENTATION; COMPARATIVE STUDIES; COMPUTATIONAL BIOLOGY; COMPUTATIONAL INTELLIGENCE; CROSS VALIDATIONS; DATA SETS; DISCRIMINATIVE ABILITY; HIGH THROUGHPUTS; PREDICTION ACCURACY; PROTEIN FUNCTIONS; PROTEIN LOCALIZATION; PROTEIN SEQUENCING; PROTEIN SUBCELLULAR LOCALIZATION; SUB-CELLULAR LOCALIZATION; SUBCELLULAR LOCATIONS; VOTING SCHEMES;

FEATURE EXTRACTION;

EID: 50249103212     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CIBCB.2006.330991     Document Type: Conference Paper

References (29)

1. K. Nishikawa, Y. Kubota, and T. Ooi, "Classification of proteins into groups based on amino acid compostion and other characters," J. Biochem., vol. 94, pp. 997-1007, 1983.
2. A. Reinhardt and T. Hubbard, "Using neural networks for prediction of subcellular location of proteins," Nucleic Acids Research, vol. 26, pp. 2230-2236, 1998.
3. K. C. Chou and D. W. Elrod, "Protein subcellular location prediction," Protein Engineering, vol. 12, pp. 107-118, 1999.
4. K. C. Chou, "Prediction of protein cellular attributes using pseudo-amino acid composition," Proteins: Structure, Function, and Genetics, vol. 43, pp. 246-255, 2001.
5. S. Hua and Z. Sun, "Support vector machine approach for protein subcellular localization prediction," Bioinformatics, vol. 17, pp. 721-728, 2001.
6. Z. P. Feng, "Prediction of the subcellular location of prokaryotic proteins based on a new representation of the amino acid composition," Biopolymers, vol. 58, pp. 491-499, 2001.
7. K. J. Park and M. Kanehisa, "Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs," Bioinformatics, vol. 19, pp. 1656-1663, 2003.
8. O. Emanuelsson, H. Nielsen, S. Brunak, and G. Heijne, "Predicting subcellular localization of proteins based on their N-terminal amino acid sequence," J. Mol. Biol., vol. 300, pp. 1005-1016, 2000.
9. H. Nielsen, J. Engelbrecht, S. Brunak, and G. Heijne, "Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites," Protein Engineering, vol. 10, pp. 1-6, 1997.
10. O. Emanuelsson, H. Nielsen, and G. Heijne, "ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage site," Protein Science, vol. 8, pp. 978-984, 1999.
11. H. Bannai, Y. Tamada, O. Maruyama, K. Nakai, and S. Miyano, "Extensive feature detection of N-terminal protein sorting signals," Bioinformatics, vol. 18, pp. 298-305, 2002.
12. C. Leslie, E. Eleazar, and W. S. Noble, "The spectrum kernel: a string kernel for SVM protein classification," in Proceedings of the Pacific Symposium on Biocomputing, vol. 7, 2002, pp. 566-575.
13. C. Leslie, E. Eskin, J. Weston, and W. S. Noble, "Mismatch string kernel for SVM protein classification," in Advances in Neural Information Processing Systems 15. MIT Press, 2003, pp. 1417-1424.
14. S. Menchetti, F. Costa, and P. Frasconi, "Weighted decomposition kernels," in Proceedings of International Conference on Machine Learning, 2005, pp. 585-592.
15. Y. Yang and B. L. Lu, "Extracting features from protein sequences using chinese segmentation techniques for subcellular localization," in Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005), 2005, pp. 288-295.
16. K. S. Toh, M. N. Nguyen, and J. C. Rajapakse, "LVQ approach using AA indices for protein subcellular localization prediction," in Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005), 2005, pp. 296-302.
17. The Gene Ontology Consortium, "Gene ontology: tool for the unification of biology," Nature Genet, vol. 25, pp. 25-29, 2000.
18. K. C. Chou and Y. D. Cai, "Prediction of protein subcellular locations by GO-FunD-PseAA predictor," Biochemical and Biophysical Research Communications, vol. 320, pp. 1236-1239, 2004.
19. Y. D. Cai and K. C. Chou, "Predicting 22 protein localizations in budding yeast," Biochemical and Biophysical Research Communications, vol. 323, pp. 425-428, 2004.
20. K. C. Chou and Y. D. Cai, "Predicting protein localization in budding yeast," Bioinformatics, vol. 21, pp. 944-950, 2005.
21. A. Höglund, P. Donnes, T. Blum, H. Adoplh, and O. Kohlbacher, "Using N-terminal targeting sequences, amino acid composition, and sequence motifs for predicting protein subcellular localization," in Proceedings of the German Conference on Bioinformatics (GCB '05), 2005, pp. 45-59.
22. A. Höglund, T. Blum, S. Brady, P. Donnes, J. S. Miguel, M.Rocheford, and et al., "Significantly improved prediction of subcellular localization by integrating text and protein sequence data," in Proceedings of Pacific Symposium on Biocomputing, vol. 11, 2006, pp. 16-27.
23. A. Höglund, P. Donnes, T. Blum, H. Adoplh, and O. Kohlbacher, "MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition," Bioinformatics, vol. 22, pp. 1158-1165, 2006.
24. Y. Yang and J. O. Pedersen, "A comparative study on feature selection in text categorization," in Proceedings of International Conference on Machine Learning, 1997, pp. 412-420.
25. R. A. Fisher, "The use of multiple measurements in taxonomic problems," Annals of Eugenics, vol. 7, pp. 179-188, 1936.
26. S. Dudoit, J. Fridlyand, and T. P. Speed, "Comparison of discrimination methods for the classification of tumors using gene expression data," Journal of the American Statistical Association, vol. 97, pp. 77-87, 2002.
27. A. Bairoch and R. Apweiler, "The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000," Nucleic Acids Research, vol. 28, pp. 45-48, 2000.
28. D. D. Lewis, "Evaluating and optimizing autonomous text classfication systems," in Proceedings of the 18th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '95), 1995, pp. 246-254.
29. C.-C. Chang and C.-J. Lin, LIBSVM: a library for support vector machines, 2001, software available at http://www.csie.ntu.edu.tw/ cjlin/libsvm.