An alignment-free method for classification of protein sequences

Protein and Peptide Letters

Volumn 14, Issue 7, 2007, Pages 647-657

  Deshmukh, Sandeep ^a   Khaitan, Sanjeet ^a   Das, Debasish ^a   Gupta, Manish ^a   Wangikar, Pramod P ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

Alignment free classification; Amino acid association rules; Dipeptide frequency; Protein sequence classification; Remote homology detection

Indexed keywords

PROTEIN;

ARTICLE; CHEMISTRY; CLASSIFICATION; PROTEIN CONFORMATION;

PROTEIN CONFORMATION; PROTEINS;

EID: 34548670505     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986607781483804     Document Type: Article

References (35)

1. Federico Abascal, A. V. (2003) Proteins: Structure, Function, and Genetics, 53, 683-692.
2. Needleman, S. B. & Wunsch, C. D. (1970) J. Mol. Biol., 48, 443-453.
3. Smith, T. F. & Waterman, M. S. (1981) J. Mol. Biol., 147, 195-197.
4. Lipman, D. J. & Pearson, W. R. (1985) Science, 227, 1435-1441.
5. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) J Mol. Biol., 215, 403-410.
6. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucl. Acid. Res., 25, 3389-3402.
7. Henikoff, S. & Henikoff, J. G. (1992) Proc. Nat. Acad. Sci. USA, 89, 10915-10919.
8. Dayhoff, M., Schwartz, R. & Orcutt, B. (1978) Atlas Protein Seq. Struct., 5, 345-358.
9. Gribskov, M., McLachlan, A. D. & Eisenberg, D. (1987) Proceedings of the National Academy of Sciences of the United States of America 84, 4355-4358.
10. Krogh, A., Brown, M., Mian, I., Sjolander, K. & Haussler, D. (1994) J. Mol. Biol., 235, 1501-31.
11. Hughey, R. & Krogh, A. (1996) CABIOS , 12, 95-107.
12. Karplus, K., Barrett, C. & Hughey, R. (1998) Bioinformatics, 14, 846-856.
13. Eddy, S. R. (1998) Bioinformatics Rev., 14(9), 755-763.
14. Ben-Hur, A. (2003) Bioinformatics, 19, 26-33.
15. Burges, C. (1998) Data Mining and Knowledge Discovery, 2, 121-167.
16. Vinga, S. & Almeida, J. (2003) Bioinformatics, 19, 513-523.
17. Leslie, C., Eskin, E. & Noble, W. S. (2002) Pacific Symposium on Biocomputing. (Altman R.B. Ed.). pp. 564-575, World Sci., Singapore
18. Leslie, C., Kuang, R. & Eskin, E. (2003) MIT Press, Cambridge.
19. Petrilli, P. (1993) CABIOS, 9, 205-209.
20. Park, K.-J. & Kanehisa, M. (2003) Bioinformatics 19, 1656-1663.
21. Tung, T. Q., Lee, D., Kim, D.-W. & Lim, J.-T. (2005) Lect. Notes in Artificial Intelligence (Subseries of Lect. Notes in Comp. Sci.), 3518, 180-185.
22. Jaakkola, T., Diekhans, M. & Haussler, D. (1999) In Proceedings of International Conference on Intelligent Systems for Molecular Biology, pp. 149-158.
23. Liao, L. & Noble, W. S. (2003) J. Comput. Biol., 10, 857-868.
24. Tendulkar, A. V., Joshi, A. A., Sohoni, M. A. & Wangikar, P. P. (2004) J. Mol. Biol., 338, 611-629.
25. Tendulkar, A. V., Wangikar, P. P., Sohoni, M. A., Samant, V. V. & Mone, C. Y. (2003) J. Mol. Biol., 334, 157-172.
26. Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E. L. L., Studholme, D. J., Yeats, C. & Eddy, S. R. (2004) Nucl. Acid. Res., 32, D138-D141.
27. Dash, M. & Liu, H. (1997) Intell. Data Anal., 1, 131-156.
28. Guyon, I. & Elisseeff, A. (2003) The J. Machine Learning Res., 3, 1157-1182.
29. Mitchell, T. M. (1997) Machine Learning, McGraw Hill, New York.
30. Hall, M. A. (1999) Working Paper 99/4, Dept. Computer Sci, University of Waikato, Hamilton, New Zealand.
31. Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J. P., Chothia, C. & Murzin, A. G. (2004) Nucl. Acid. Res., 32, D226-D229.
32. Witten, I. & Frank, E. (2000) Data mining: practical machine learning tools and techniques with Java implementations. Morgan Kaufmann Publishers Inc., San Francisco, USA.
33. Krause, D. S. & Van Etten, R. A. (2005) New England J. Med., 353, 172-187.
34. Richardson, J. S. (1981) Advan. Prot. Chem. 34, 167-339.
35. Chandonia, J.-M., Hon, G., Walker, N. S., Lo Conte, L., Koehl, P., Levitt, M. & Brenner, S. E. (2004) Nucl. Acid. Res., 32, D189-D192.