Stochastic context-free grammers for tRNA modeling

Nucleic Acids Research

Volumn 22, Issue 23, 1994, Pages 5112-5120

  Sakakibara, Yasubumi ^a   Brown, Michael ^a   Hughey, Richard ^a,b   Mian, I Saira ^a,c   Sjölander, Kimmen ^a   Underwood, Rebecca C ^a   Haussler, David ^a  

^a Computer and Information Sciences ^*  (United States)

^b Computer Engineering ^*  (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

ARTICLE; MOLECULAR MODEL; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE;

ALGORITHMS; BASE SEQUENCE; COMPUTER SIMULATION; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, TRANSFER; SEQUENCE ALIGNMENT; STOCHASTIC PROCESSES; SUPPORT, U.S. GOV'T, NON-P.H.S.; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0028593508     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/22.23.5112     Document Type: Article

References (59)

1. J. E. Dahlberg and J. N. Abelson, (ed.) (1989) RNA processing. Pan A. General Methods, Methods in Enzymology 180. Academic Press, New York.
2. R. F. Doolittle, (ed.) (1990) Molecular Evolution, Methods in Enzymology 183. Academic Press, New York.
3. Haussler, D., Krogh, A., Mian, I. S., and Sjolander, K. (1993) In Proceedings of the Hawaii International Conference on System Sciences 1. Los Alamitos, CA: IEEE Computer Society Press, pp. 792 - 802.
4. Krogh, A., Brown, M., Mian, I. S., Sjolander, K., and Haussler, D. (1994) Journal of Molecular Biology 235, 1501-1531.
5. Krogh, A., Mian, I. S., and Haussler, D. (1994) Nucleic Acids Research 22, 4768 - 4778.
6. Fox, G. E. and Woese, C. R. (1975) Nature 256, 505-507.
7. Woese, C. R., Gutell, R. R., Gupta, R., and Noller, H. F. (1983) Microbiology Reviews 47(4), 621-669.
8. James, B. D., Olsen, G. J., and Pace, N. R. (1989) Methods in Enzymology 180, 227 -239.
9. Tinoco Jr., I., Uhlenbeck, O. C., and Levine, M. D. (1971) Nature 230, 363-367.
10. Turner, D. H., Sugimoto, N., and Freier, S. M. (1988) Annual Review of Biophysics and Biophysical Chemistry 17, 167—192.
11. Gouy, M. (1987) In M. J. Bishop and C. R. Rawlings, (ed.), Nucleic acid and protein sequence analysis, a practical approach, pp. 259 —284IRL Press Oxford, England.
12. Zuker, M. (1989) Science 244, 48 - 52.
13. Waterman, M. S. (1989) In M. S. Waterman, (ed.), Mathematical Methods for DNA Sequences, chapter 8 CRC Press.
14. Le, S. Y. and Zuker, M. (1991) J. Biomolecular Structure and Dynamics 8, 1027-1044.
15. Han, K. and Kim, H.-J. (1993) NAR 21, 1251-1257.
16. Chiu, D. K. and Kolodziejczak, T. (1991) CABIOS 7, 347 - 352.
17. Sankoff, D. (1985) S1AM J. Appl. Math. 45, 810-825.
18. Winker, S., Overbeek, R., Woese, C, Olsen, G., and Pfluger, N. (1990) CABIOS 6, 365 - 371.
19. Klinger, T. and Brutlag, D. (1993) In Lawrence Hunter, David Searls, and Jude Shavlik, (ed.), First International Conference on Intelligent Systems for Molecular Biology, Menlo Park: AAAI Press.
20. Gutell, R. R., Power, A., Hertz, G. Z., Putz, E. J., and Stormo, G. D. (1992) NAR 20, 5785 - 5795.
21. Staden, R. (1990) In Doolittle (2) pp. 193-211.
22. Lathrop, R. H., Webster, T. A., and Smith, T. F. (1987) Communications of the ACM 30(11), 909 -921.
23. Sibbald, P. R. and Argos, P. (1990) CAB/OS 6(3), 279-288.
24. Abarbanel, R. M., Wieneke, P. R., Mansfield, E., Jaffe, D. A., and Brutlag, D. L. (1984) NAR 12(1), 263-280.
25. Saurin, W. and Marliere, P. (1987) CABIOS 3(2), 115-120.
26. Gautheret, D., Major, F., and Cedergren, R. (1990) CAB/OS6(4), 325-331.
27. Cohen, F. E., Abarbanel, R. M., Kuntz, I. D., and Fletterick, R. J. (1986) Biochemistry 25, 266-276.
28. Presnell, S. R. and Cohen, F. E. (1993) Annual Review of Biophysics and Biomolecular Structure 22, 283-298.
29. Eddy, S. R. and Durbin, R. (1994) Nucleic Acids Research 22, 2079 - 2088.
30. Macke, T., Cohen, P., Grate, L., Mian, I., and Noller, H. F. (in preparation) (1994).
31. Fichant, G. A. and Burks, C. (1991) JMB 220, 659 - 671.
32. Staden, R. (1980) NAR 8, 817 - 825.
33. Marvel, C. C. (1986) NAR 14, 431-435.
34. Searls, D. B. (1992) American Scientist 80, 579-591.
35. Baker, J. K. (1979) Speech Communication Papers for the 97th Meeting of the Acoustical Society of America pp. 547-550.
36. Searls, D. B. (1993) In L. Hunter, (ed.), Artificial Intelligence and Molecular Biology, chapter 2, pp. 47-120 AAAI Press.
37. Searls, D. B. and Dong, S. (1993) In H. A. Lim, J. Fickett, C. R. Cantor, and R. J. Robbins, (ed.), Proceedings of the 2nd International Conference on Bioinformatics, Supercomputing, and Complex Genome Analysis, World Scientific: pp. 89-101.
38. Sakakibara, Y., Brown, M., Hughey, R., Mian, I. S., Sjolander, K., Underwood, R. C, and Haussler, D. (1994) In Proceedings of the Asilomar Conference on Combinatorial Pattern Matching New York, NY: Springer-Verlag. In press.
39. Sakakibara, Y., Brown, M., Hughey, R., Mian, I. S., Sjolander, K., Underwood, R., and Haussler, D. The application of stochastic context-free grammars to folding, aligning and modeling homologous RNA sequences Technical Report UCSC-CRL-94-14 University of California, Santa Cruz Computer and Information Sciences Dept., Santa Cruz, CA 95064 (1993).
40. Steinberg, S., Misch, A., and Sprinzl, M. (1993) NAR 21, 3011-3015.
41. Lari, K. and Young, S. J. (1990) Computer Speech and Language 4, 35-56.
42. Hopcroft, J. and Ullman, J. (1979) Introduction to Automata Theory, Languages and Computation, Addison-Wesley,.
43. Rabiner, L. R. (1989) Proc IEEE 77(2), 257-286.
44. Zuker, M. and Sankoff, D. (1984) Bull. Math. Biol. 46, 591-621.
45. Waterman, M. S. (1988) Methods in Enzymology 164, 765 - 792.
46. Weiser, B., Gutell, R., and Noller, H. F. In preparation (1994).
47. Michel, F. and Westhof, E. (1990) JMB 216, 585 - 610.
48. Michel, F., Ellington, A. D., Couture, S., and Szostak, J. W. (1990) Nature 347, 578 - 580.
49. Michel, F., Umesono, K., and Ozeki, H. (1989) Gene 82, 5-30.
50. Brown, J. W., Haas, E. S., James, B. D., Hunt, D. A., Liu, J. S., and Pace, N. R. (1991) J. Bact. 173, 3855-3863.
51. Tranguch, A. J. and Engelke, D. R. (1993) JBC 268, 14045-1455.
52. Guthrie, C. and Patterson, B. (1988) Ann. Rev. Gen. 22, 387-419.
53. Zwieb, C. (1989) Prog. Nuc. Acids. Res. Mol. Biol. 37, 207-234.
54. Lathrop, R. H. and Smith, T. F. (1994) In Proceedings of the 27th Hawaii International Conference on System Sciences Los Alamitos, CA: IEEE Computer Society Press.
55. Grate, L., Herbster, M., Hughey, R., Mian, I., Noller, H., and Haussler, D. (1994) In Proc. of Second Int. Conf. on Intelligent Systems for Molecular Biology Menlo Park, CA: AAAI/MIT Press.
56. Sakakibara, Y., Brown, M., Mian, I. S., Underwood, R., and Haussler, D. (1994) In Proceedings of the Hawaii International Conference on System Sciences Los Alamitos, CA: IEEE Computer Society Press.
57. Fu, K. S. (1982) Syntactic pattern recognition and applications, Prentice-Hall, Englewood Cliffs, NJ.
58. Engelfriet, J. and Rozenberg, G. (1991) In E. Ehrig, H.J. Kreowski, and G. Rozenberg, (ed.), Lecture Notes in Computer Science, 532. pp. 12-23 Springer-Verlag.
59. Steinberg, S., Gautheret, D., Cedergren, R., and Sprinzl, M. (1993) In D. Soil and U. L. RajBhandary, (ed.), Transfer RNA, American Society of Microbiology Washington DC.