Finding the most significant common sequence and structure motifs in a set of RNA sequences

Nucleic Acids Research

Volumn 25, Issue 18, 1997, Pages 3724-3732

  Gorodkin, J ^a   Heyer, L J ^b   Stormo, G D ^b  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ALGORITHM; ARTICLE; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SCORING SYSTEM; SEQUENCE HOMOLOGY;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; DATABASES, FACTUAL; HUMANS; RNA; SEQUENCE ANALYSIS;

EID: 0030812919     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/25.18.3724     Document Type: Article

References (40)

1. Tuerk, C. and Gold, L. (1990) Science 249, 505-510.
2. Gorodkin, J., Heyer, L. J., and Stormo, G. D. (1997) In T. Gaasterland, P. Karp, K. Karplus, C. Ouzounis, C. Sander, and A. Valencia (eds), Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, CA. pp. 120-123.
3. Smith, T. F. and Waterman, M.S. (1981) J. Mol. Biol. 147, 195-197.
4. Waterman, M. S. and Eggert, M. (1987) J. Mol. Biol. 197, 723-728.
5. Higgins, D. G., Bleasby, A.J. and Fuchs, R. (1991) Comput. Appl. Biosci. 8, 189-191.
6. Thompson, J. D., Higgins, D. G. and Gibson, T. J. (1994) Nucleic Acids Res 22, 4673-4680.
7. Lipman, D., Altschul, S. and Kececioghlu, J. (1994) Proc. Natl Acad. Sci. USA 86, 4412-4415.
8. Baldi, P., Chauvin, Y., Hunkapiller, T. and McClure, M. A. (1994) Proc. Natl. Acad. Sci. USA 91, 1059-1063.
9. Krogh, A., Brown, M., Mian, I. S., Sjölander, K. and Haussler, D. (1994) J. mol. Biol. 235, 1501-1531.
10. Nussinov, R. and Jacobson, A. B. (1980) Proc. Natl. Acad. Sci. USA 77, 6309-6313.
11. Zuker, M. and Stiegler, P. (1981) Nucleic Acids Res. 9, 133-148.
12. Hotacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., and Schuster, P. (1994) Monatshefte für Chemie 125, 167-188 (http://www.tbi.univie.ac.at/~ivo/RNA/).
13. Kim, J., Cole, J. R. and Pramanik, S. (1996) Comput. Appl. Biosci. 12, 250-267.
14. Schmilz, M. and Steger, G. (1996) J. Mol. Biol. 255, 254-266.
15. Gultyaev, A. R., vanBatenburg, F. H. D. and Pleij, C. W. A. (1995) J. Mol. Biol. 250, 37-51.
16. Westhof, E. and Michel, F. (1994) In K. Nagai and I. W. Mattaj (eds), RNA-Protein Interactions. IRL Press at Oxford University Press, Oxford, UK. pp. 26-51.
17. Westhof, E., Auffinger, P. and Gaspin, C. (1996) In M. J. Bishop and C. J. Rawlings (eds), DNA-Protein Sequence Analysis. IRL Press at Oxford University Press, Oxford, UK. pp. 255-278.
18. Eddy, S. and Durbin, R. (1994) Nucleic Acids Res. 22, 2079-2088 (http://genome.wustl.edu/eddy/\#cove).
19. Sakakibara, Y., Brown, M., Hughey, R., Mian, I. S., Sjölander, K., Underwood, R. C. and Haussler, D. (1994) Nucleic Acids Res. 22, 5112-5120.
20. Stormo, G. D. and Hartzell, G. W.,III (1989) Proc. Natl. Acad. Sci. USA 86, 1183-1187.
21. Hertz, G. Z., Hartzell, G. W.,III and Stormo, G. D. (1990) Comput Appl. Biosci. 6, 81-92.
22. Heumann, J. M., Lapedes, A. S. and Stormo, G. D. (1994) In Altman, R., Brutlag, D., Karp, P., Lathrop, R. and Searls, D. (eds), Proceedings of the Second International Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, CA. pp. 188-194.
23. Heumann, J. M., Lapedes. A. S., and Stormo, G. D. (1995) In Proceedings of the 1995 World Congress on Neural Networks II. INNS Press, Washington, DC. pp. 771-775.
24. Sankoff, D. (1985) SIAM J. Appl. Math. 45, 810-825.
25. Cary, R.B. and Stormo, G. D. (1995) In Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. and Wodak, S. (eds), Proceedings of the Third International Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, CA. pp. 75-80.
26. Tabaska, J. E. and Stormo, G. D. (1997) In T. Gaasterland, P. Karp, K. Karplus, C. Ouzounis, C. Sander, and A. Valencia (eds) Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, CA. pp. 311-318.
27. Tuerk, C., MacDougal, S., Hertz, G. Z. and Gold, L. (1992) In F. Ferré, K. Mullis, R. Gibbs, and A. Ross (eds), The Polymerase Chain Reaction. Birkhauser, Springer-Verlag, NY.
28. Tuerk, C., MacDougal, S., and Gold, L. (1992) Proc. Natl. Acad. Sci. USA 89, 6988-6992.
29. Jenison, R. D., Gill, S. C., Pardi, A. and Polisky, B. (1994) Science 263, 1425-1429.
30. Schneider, D., Tuerk, C., and Gold, L. (1992) J. Mol. Biol. 228, 862-869.
31. Gotoh, O. (1982) J. Mol. Biol. 162, 705-708.
32. Feng, D.-F. and Doolittle, R. F. (1987) J. Mol. Evol. 25, 351-360.
33. Schneider, T. D. and Stephens, R. M. (1990) Nucleic Acids Res. 18, 6097-6100.
34. Sakakibara, Y., Brown, M., Underwood, R. C., Mian, I. S. and Haussler, D. (1994) In L. Hunter (ed.), Proceedings of the Twenty-Seventh Annual Hawaii International Conference on System Sciences: Biotechnology Computing, vol. V. IEEE Computer Society Press, Los Alamitos, CA. pp. 284-293.
35. McCaskill, J. S. (1990) Biopolymers 29, 1105-1119.
36. Turner, D. H., Sugimoto, N. and Freier, S. M. (1988) Annu. Rev. Biophys. Biophys. Chem. 17, 167-192.
37. Shapiro, B. A. (1988) Comput. Appl. Biosci. 4, 381-393.
38. Shapiro, B. A. and Zhang, K. (1990) Comput. Appl. Biosci. 6, 309-318.
39. Fontana, W., Konings, D. A. M., Stadler, P. F. and Schuster, P. (1993) Biopolymers 33, 1389-1404.
40. Gorodkin, J., Heyer, L. J., Brunak, S. and Stormo, G. D. (1997) Comput. Appl. Biosci., in press (http://www.cbs.dtu.dk/gorodkin/appl/slogo.html).