Profile-based string kernels for remote homology detection and motif extraction

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Volumn , Issue , 2004, Pages 152-160

  Kuang, Rui ^a   Ie, Eugene ^a,b   Wang, Ke ^a   Wang, Kai ^b   Siddiqi, Mahira ^b   Freund, Yoav ^a,b   Leslie, Christina ^a,b,c  

^a Columbia University ^*  (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

^c NONE   (United States)

Author keywords

Kernels; Protein classification; Protein motifs; Support vector machine

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; COMPUTER SCIENCE; CONFORMAL MAPPING; DATA STRUCTURES; DATABASE SYSTEMS; MARKOV PROCESSES; MATHEMATICAL MODELS; OPTIMIZATION; PROBABILITY; PROTEINS; VECTORS;

KERNELS; PROTEIN CLASSIFICATION; PROTEIN MOTIFS; SUPPORT VECTOR MACHINES (SVM);

BIOMEDICAL ENGINEERING;

EID: 14044266328     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (21)

1. S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25:3389-3402, 1997.
2. P. Baldi, Y. Chauvin, T. Hunkapiller, and M. A. McClure. Hidden markov models of biological primary sequence information. PNAS, 91(3):1059-1063, 1994.
3. A. Ben-Hur and D. Brutlag. Remote homology detection: a motif based approach. Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, 2003.
4. B. E. Boser, I. Guyon, and V. Vapnik. A training algorithm for optimal margin classifiers. In Fifth Annual Workshop on Computational Learning Theory, pages 144-152, Pittsburg, PA, 1992. ACM Press.
5. C. Bystroff and D. Baker. Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of Molecular Biology, 281:565-577, 1998.
6. S. R. Eddy. Multiple alignment using hidden markov models. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pages 114-120. AAAI Press, 1995.
7. M. Gribskov, A. D. McLachlan, and D. Eisenberg. Profile analysis: Detection of distantly related proteins. PNAS, 84:4355-4358, 1987.
8. M. Gribskov and N. L. Robinson. Use of receiver operating characteristic (roc) analysis to evaluate sequence matching. Computers and Chemistry, 20(1):25-33, 1996.
9. Y. Hou, W. Hsu, M. L. Lee, and C. Bystroff. Efficient remote homology detection using local structure. Bioinformatics, 19(17):2294-2301, 2003.
10. J. Y. Huang and D. L. Brutlag. The emotif database. Nucleic Acids Res., 29:202-204, 2001.
11. M. Hyvonen, M. J. Macias, M. Nilges, H. Oschkinat, M. Saraste, and M. Wilmanns. Structure of the binding site for inositol phosphates in a ph domain. EMBO J, 14:4676, 1995.
12. T. Jaakkola, M. Diekhans, and D. Haussler. A discriminative framework for detecting remote protein homologies. Journal of Computational Biology, 7(1/2):95-114, 2000.
13. V. A. Jaravine, D. E. Nolde, M. J. Reibarkh, Y. V. Korolkova, S. A. Kozlov, K. A. Pluzhnikov, E. V. Grishin, and A. S. Arseniev. Three-dimensional structure of toxin oskl from orthochirus scrobiculosus scorpion venom. Biochemistry, 36(6):1223-32, 1997.
14. A. Krogh, M. Brown, I. Mian, K. Sjolander, and D. Haussler. Hidden markov models in computational biology: Applications to protein modeling. Journal of Molecular Biology, 235:1501-1531, 1994.
15. C. Leslie, E. Eskin, A. Cohen, J. Weston, and W. S. Noble. Mismatch string kernels for discriminative protein classification. Bioinformatics, 2004. To appear.
16. C. Leslie, E. Eskin, J. Weston, and W. S. Noble. Mismatch string kernels for SVM protein classification. Advances in Neural Information Processing Systems 15, pages 1441-1448, 2003.
17. C. Leslie and R. Kuang. Fast kernels for inexact string matching. Sixteenth Annual Conference on Learning Theory and Seventh Kernel Workshop, pages 114-128, 2003.
18. L. Liao and W. S. Noble. Combining pairwise sequence similarity and support vector machines for remote protein homology detection. In Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology, pages 225-232, Washington, DC, 2002. ACM Press.
19. C. G. Nevill-Manning, T. D. Wu, and D. L. Brutlag. Highly specific protein sequence motifs for sequence analysis. Proceedings of the National Academy of Sciences 95, pages 5865-5871, 1998.
20. K. Tsuda, M. Kawanabe, G. Rtsch, S. Sonnenburg, and K. Müller. A new discriminative kernel from probabilistic models. Neural Computation, 14:2397-2414, 2002.
21. J. Weston, C. Leslie, D. Zhou, A. Elisseeff, and W. S. Noble. Cluster kernels for semi-supervised protein classification. Neural Information Processing Systems 17, 2003.