RNA sequence analysis using covariance models

Nucleic Acids Research

Volumn 22, Issue 11, 1994, Pages 2079-2088

  Eddy, Sean R ^a   Durbin, Richard ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

ALGORITHM; ARTICLE; CONSENSUS SEQUENCE; COVARIANCE; DATA BASE; PRIORITY JOURNAL; PROBABILITY; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; STATISTICAL MODEL;

ALGORITHMS; ANIMAL; BASE SEQUENCE; CAENORHABDITIS ELEGANS; CONSENSUS SEQUENCE; INFORMATION SYSTEMS; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, TRANSFER; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SUPPORT, NON-U.S. GOV'T;

EID: 0028272315     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/22.11.2079     Document Type: Article

References (67)

1. Bork, P., Ouzounis, C., Sander, C., Scharf, M., Schneider, R., and Sonnhammer, E. (1992) Protein Science, 1, 1677-1690.
2. Green, P., Lipman, D., Hillier, L., Waterston, R., Slates, D., and Claverie, J.-M. (1993) Science, 259, 1711-1716.
3. Oliver, S., van derAart, Q., Agostoni-Carbone, M., Aigle, M., et al. (1992) Nature, 357, 38-46.
4. Sulston, J., Du, Z., Thomas, K., Wilson, R., Hillier, L., Staden, R., Halloran, N., Green, P., Thierry-Mieg, J., Qiu, L., Dear, S., Coulson, A., Craxton, M., Durbin, R., Berks, M., Metzstein, M., Hawkins, T., Ainscough, R., and Waterston, R. (1992) Nature, 356, 37-41.
5. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. J. Mol. Biol., 215, 403 -410.
6. Pearson, W. and Lipman, D. (1988) Proc. Natl. Acad. Sci. USA, 85, 2444-2448.
7. Barton, G. J. (1990) Meth. Enzymol., 183, 403-427.
8. Gribskov, M., Luthy, R., and Eisenberg, D. (1990) Meth. Enzymol., 183, 146-159.
9. Baldi, P., Chauvin, Y., Hunkapiller, T., and McClure, M. A. (1994) Proc. Natl. Acad. Sci. USA, 91, 1059-1063.
10. Krogh, A., Brown, M., Mian, I. S., Sjolander, K., and Haussler, D. (1994) J. Mol. Biol., 235, 1501-1531.
11. Schimmel, P. R. Soil, D. and Abelson, J. N. (eds) (1979) Transfer RNA: Structure, Properties, and Recognition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
12. Steinberg, S., Misch, A., and Sprinzl, M. (1993) Nucleic Acids Res., 21, 3011-3015.
13. Larsen, N. and Zwieb, C. (1993) Nucleic Acids Res., 21, 3019-3020.
14. Lambowitz, A. M. and Belfort, M. (1993) Ann. Rev. Biochem., 62, 587-622.
15. Michel, F., Netter, P., Xu, M.-Q., and Shub, D. (1990) Genes Dev., 4, 777-788.
16. Guthrie, C. and Patterson, B. (1988) Ann. Rev. Genet., 22, 387-419.
17. Rosen, C. A. (1991) Trends Genet., 7, 9-14.
18. Theil, E. C. (1990) J. Biol. Chem., 265, 4771-4774.
19. Ellington, A. and Szostak, J. (1990) Nature, 346, 818 -822.
20. Tuerk, C. and Gold, L. (1990) Science, 249, 505-510.
21. Bartel, D. P. and Szostak, J. W. (1993) Science, 261, 1411-1418.
22. Fichant, G. A. and Burks, C. (1991) J. Mol. Biol., 220, 659-671.
23. Lisacek, F., Diaz, Y., and Michel, F. (1994) J. Mol. Biol., 235, 1206-1217.
24. Marvel, C. C. (1986) Nucleic Acids Res., 14, 431-435.
25. Staden, R. (1980) Nucleic Acids Res., 8, 817-825.
26. Bairoch, A. (1993) Nucleic Acids Res., 21, 3097-3103.
27. Gautheret, D., Major, F., and Cedergren, R. (1990) Comput. Applic. Biosci., 6, 325-331.
28. Saurin, W. and Marliere, P. (1987) Comput. Applic. Biosci., 3, 115-120.
29. Searls, D. B. (1992) American Scientist, 80, 579-591.
30. Sakakibara, Y., Brown, M., Underwood, R. C., Mian, I. S., and Haussler, D. (1994) In Hunter, L. (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.
31. Gutell, R., Power, A., Hertz, G., Putz, E., and Stormo, G. (1992) Nucleic Acids Res., 20, 5785-5795.
32. Woese, C. R. and Pace, N. R. (1993) In Gesteland, R.F. and Atkins, J.F. (eds), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
33. Robertson, D. and Joyce, G. (1990) Nature, 344, 467-468.
34. Shapiro, B. A. and Zhang, K. (1990) Comput. Applic. Biosci., 6, 309-318.
35. tenDam, E., Pleij, K., and Draper, D. (1992) Biochemistry, 31, 11665-11676.
36. Rabiner, L. R. (1989) Proc. IEEE, 77, 257-286.
37. Knuth, D. E. (1973) The Art of Computer Programming: Fundamental Algorithms, 2nd edition, Vol. 1. Addison—Wesley, Reading, MA.
38. Nussinov, R., Pieczenik, G., Griggs, J. R., and Kleitman, D. J. (1978) SIAM J. Appl. Math., 35, 68-82.
39. Zuker, M. and Stiegler, P. (1981) Nucleic Acids Res., 9, 133-148.
40. Lari, K. and Young, S. (1990) Computer Speech and Language, 4, 35-56.
41. Lari, K. and Young, S. (1991) Computer Speech and Language, 5, 237-257.
42. Chiu, D. K. and Kolodziejczak, T. (1991) Comput. Applic. Biosci., 7, 347-352.
43. Han, K. and Kim, H.-J. (1993) Nucleic Acids Res., 21, 1251 -1257.
44. Zuker, M. (1989) Science, 244, 48-52.
45. Berg, O. G. and vonHippel, P. H. (1987) J. Mol. Biol., 193, 723-750.
46. Needleman, S. and Wunsch, C. (1970) J. Mol. Biol., 48, 443 -453.
47. Higgins, D., Bleasby, A., and Fuchs, R. (1992) Comput. Applic. Biosci., 8, 189-191.
48. Schneider, T. D., Stormo, G. D., Gold, L., and Ehrenfeucht, A. (1986) J. Mol. Biol., 188, 415 -431.
49. Kim, S.-H. (1979) In Schimmel, P.R., Soil, D., and Abelson, J.N. (eds), Transfer RNA: Structure, Properties, and Recognition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
50. Daniels, G. R. and Deininger, P. L. (1985) Nature, 317, 819-822.
51. Okimoto, R. and Wolstenholme, D. R. (1990) EMBO J., 9, 3405-3411.
52. Cech, T. R. and Bass, B. L. (1986) Ann. Rev. Biochem., 55, 599 -629.
53. Michel, F., Umesono, K., and Ozeki, H. (1989) Gene, 82, 5-30.
54. Symons, R. H. (1992) Ann. Rev. Biochem., 61, 64-671.
55. Konings, D. and Hogeweg, P. (1989) J. Mol. Biol., 207, 597 -614.
56. Brown, J. W., Haas, E. S., James, B. D., Hunt, D. A., and Pace, N. R. J. Bacteriol., 173, 3855-3863.
57. Fox, G. E. and Woese, C. R. (1975) Nature, 256, 505-507.
58. Michel, F. and Westhof, E. (1990) J. Mol. Biol., 216, 585-610.
59. Noller, H. F. and Woese, C. R. (1981) Science, 212, 403 -411.
60. Noller, H. F., Kop, J., Wheaton, V., Brosius, J., Gutell, R. R., Kopylov, A. M., Dohme, F., Herr, W., Stahl, D. A., Gupta, R., and Woese, C. R. (1981) Nucleic Acids Res., 9, 6167-6189.
61. Zwieb, C. (1989) Prog. Nucl. Acid Res. Mol. Biol., 37, 207-234.
62. Fournier, M. J. and Maxwell, E. S. (1993) Trends Biochem. Sci., 18, 131-135.
63. Sankoff, D. (1985) SIAM J. Appl. Math., 45, 810-825.
64. Chomsky, N. (1959) Information and Control, 2, 137-167.
65. Gersting, J. L. (1993) Mathematical Structures for Computer Science, Chapter W.H. Freeman, New York, NY.
66. Mac Kay, D. J. (1992) Neural Computation, 4, 415 -447.
67. Brenner, S. and Lemer, R. (1992) Proc. Natl. Acad. Sci. USA, 89, 5381-5383.