Subcellular localization prediction with new protein encoding schemes

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 4, Issue 2, 2007, Pages 227-232

  Oǧul, Hasan ^a   Mumcuoǧlu, Erkan Ü ^b  

^a BASKENT UNIVERSITY   (Turkey)

^b MIDDLE EAST TECHNICAL UNIVERSITY   (Turkey)

Author keywords

n peptide composition; Probabilistic suffix tree; Subcellular localization; Support vector machines

Indexed keywords

AMINO ACIDS; DATA STRUCTURES; DECISION TREES; SUPPORT VECTOR MACHINES;

NUCLEAR PROTEINS; PROBABILISTIC SUFFIX TREES; PROTEIN ENCODING; SUBCELLULAR LOCALIZATION;

PEPTIDES;

EUKARYOTA;

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CELL FRACTIONATION; CHEMISTRY; CLASSIFICATION; EVALUATION; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; INFORMATION STORAGE AND RETRIEVAL; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SUBCELLULAR FRACTIONS;

EID: 34248383193     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2007.070209     Document Type: Article

References (30)

1. V. Atalay and R.Ç. Atalay, "Implicit Motif Distribution Based Hybrid Computational Kernel for Sequence Classification," Bioinformatics, vol. 21, pp. 1429-1436, 2005.
2. G. Bejerano and G. Yona, "Variations on Probabilistic Suffix Trees: Statistical Modeling and Prediction of Protein Families," Bioinformatics, vol. 17, pp. 23-43, 2000.
3. M. Bhasin, A. Garg, and G.P.S. Raghava, "PSLpred: Prediction of Subcellular Localization of Bacterial Proteins," Bioinformatics, vol. 21, pp. 2522-2524, 2005.
4. M. Bhasin and G.P.S. Raghava, "ESLpred: SVM-Based Method for Subcellular Localization of Eukaryotic Proteins Using Dipeptide Composition and PSI-BLAST," Nucleic Acids Research, vol. 32, pp. 415-419, 2004.
5. M. Cokol, R. Nair, and B. Rost, "Finding Nuclear Localisation Signals," EMBO Reports, vol. 1, pp. 411-415, 2000.
6. O. Emanuelson, H. Nielsen, S. Brunak, and H. Gunnar, "Predicting Subcellular Localization of Proteins Based on Their N-Terminal Amino Acid Sequence," J. Molecular Biology, vol. 300, pp. 1005-1016, 2000.
7. J.L. Gardy, M.R. Laird, F. Chen, S. Rey, C.J. Walsh, M. Ester, and F.S.L. Brinkman, "PSORTb v.2.0: Expanded Prediction of Bacterial Protein Subcellular Localization and Insights Gained from Comparative Proteome Analysis," Bioinformatics, vol. 21, pp. 617-623, 2005.
8. J.L. Gardy, C. Spencer, K. Wang, M. Ester, G.E. Tusnády, I. Simon, S. Hua, K. deFays, C. Lambert, K. Nakai, and S.L. Brinkman, "PSORT-B: Improving Protein Subcellular Localization Prediction for Gram-Negative Bacteria," Nucleic Acids Research, vol. 31, pp. 3613-3617, 2003.
9. S. Hua and Z. Sun, "Support Vector Machine Approach for Protein Subcellular Localization Prediction," Bioinformatics, vol. 17, pp. 721-728, 2001.
10. Y. Huang and Y. Li, "Prediction of Protein Subcellular Locations Using Fuzzy k-NN Method," Bioinformatics, vol. 20, pp. 21-28, 2004.
11. 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. 1656-1563, 2003.
12. L. Liao and W.S. Noble, "Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships," J. Computer Biology, vol. 10, pp. 857-868, 2003.
13. B.W. Matthews, "Comparison of Predicted and Observed Secondary Structure of T4 Phage Lysozyme," Biochimica et Biophysica Acta, vol. 405, pp. 442-451, 1975.
14. L.R. Murphy, A. Wallqvist, and R.M. Levy, "Simplified Amino Acid Alphabets for Protein Fold Recognition and Implications for Folding," Protein Eng., vol. 13, pp. 149-152, 2000.
15. R. Nair and B. Rost, "Better Prediction of Sub-Cellular Localization by Combining Evolutionary and Structural Information," Proteins, vol. 53, pp. 917-930, 2003.
16. K. Nakai and P. Horton, "PSORT: A Program for Detecting Sorting Signals in Proteins and Predicting Their Subcellular Localization," Trends in Biochemical Science, vol. 24, pp. 34-36, 1999.
17. H. Nakashima and K. Nishikawa, "Discrimination of Intracellular and Extracellular Proteins Using Amino Acid Composition and Residue-Pair Frequencies," J. Molecular Biology, vol. 238, pp. 54-61, 1994.
18. H. Oǧul and E.Ü. Mumcuoǧlu, "Prediction of Protein Subcellular Localization Using Support Vector Machines and Probabilistic Suffix Trees," Proc. First Int'l Symp. Health Informatics and Bioinformatics, pp. 56-62, 2005.
19. A. Reinhardt and T. Hubbard, "Using Neural Networks for Prediction of the Subcellular Location of Proteins," Nucleic Acids Research, vol. 26, pp. 2230-2236, 1998.
20. T.F. Smith and M.S. Waterman, "Identification of Common Molecular Subsequences," J. Molecular Biology, vol. 147, pp. 195-197, 1981.
21. D. Xie, A. Li, M. Wang, Z. Fan, and H. Feng, "LOCSVMPSI: A Web Server for Subcellular Localization of Eukaryotic Proteins Using SVM and Profile of PSI-BLAST," Nucleic Acids Research, vol. 33, pp. W105-W110, 2005.
22. V. Vapnik, The Nature of Statistical Learning Theory. Spring-Verlag, 1995.
23. K. Weis, "Importins and Exportins: How to Get In and Out of the Nucleus," Trends in Biochemical Science, vol. 67, pp. 265-306, 1998.
24. A. Garg, M. Bhasin, and G.P. Raghava, "Support Vector Machine-Based Method for Subcellular Localization of Human Proteins Using Amino Acid Compositions, Their Order, and Similarity Search," J. Biological Chemistry, vol. 280, pp. 14427-14432, 2005.
25. Z. Lei and Y. Dai, "An SVM-Based System for Predicting Protein Subnuclear Localizations," BMC Bioinformatics, vol. 6, p. 291, 2005.
26. C.S. Yu, C.J. Lin, and J.K. Hwang, "Predicting Subcellular Localization of Proteins for Gram-Negative Bacteria by Support Vector Machines Based on n-Peptide Compositions," Protein Science, vol. 13, pp. 1402-1406, 2004.
27. R. Nair and B. Rost, "Mimicking Cellular Sorting Improves Prediction of Subcellular Localization," J. Molecular Biology, vol. 348, pp. 85-100, 2005.
28. Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner, "Predicting Subcellular Localization of Proteins Using Machine-Learned Classifiers," Bioinformatics, vol. 20, pp. 547-556, 2004.
29. H. Ogul and E. Mumcuoglu, "SVM-Based Detection of Distant Protein Structural Relationships Using Pairwise Probabilistic Suffix Trees," Computational Biology and Chemistry, vol. 30, pp. 292-299, 2006.
30. H. Oǧul and E. Mumcuoǧlu, "A Discriminative Method for Remote Homology Detection Based on n-peptide Compositions with Reduced Amino Acid Alphabets," BioSystems, to appear.