Genetic sequences as product of compression by inclusive superposition of many codes

Molecular Biology

Volumn 31, Issue 4, 1997, Pages 647-654

  Trifonov, E N ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Code degeneracy; Compression; Sequence codes; Superposition

Indexed keywords

EID: 0031315298     PISSN: 00268933     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (74)

1. Schaap, T.J., Theor. Biol., 1971, vol. 32, pp. 293-298.
2. Zuckerkandl, E.J., Molec. Evol., 1976, vol. 7, pp. 167-183.
3. Zuckerkandl, E.J., Molec. Evol., 1976, vol. 7, pp. 269-312.
4. Trifonov, E.N., International Cell Biology 1980-1981, Schweiger, H., Ed., Springer, 1981, pp. 128-138.
5. Gillies, S.D., Morrison, S.L., Oi, V.T., and Tonegawa, S., Cell, 1983, vol. 33, pp. 717-728.
6. Bornstein, P., McKay, J., Morishima, J.K., Devarayalu, S., and Gelinas, R.E., Proc. Natl. Acad Sci. USA, 1984, vol. 84, pp. 8869-8873.
7. Trifonov, E.N., Bull. Math. Biol., 1989, vol. 51, pp. 417-432.
8. Zhang, K., Bosron, W.F., and Edenberg, H.J., Gene, 1987, vol. 57, pp. 27-36.
9. Perutz, M.E., Johnson, T., Suzuki, M., and Finch, J.T, Proc. Natl. Acad. Sci. USA, 1994, vol. 91, pp. 5355-5358.
10. Fresco, J.R., Alberts, B.M., and Doty, P., Nature, 1960, vol. 188, pp. 98-101.
11. Spirin, A.S., Macromolecular Structure of RNAs, Reinhold, 1964.
12. Trifonov, E.N., Math. Biosci., 1988, vol. 90, pp. 507-517.
13. Beckmann, J.S., Brendel, V., and Trifonov, E.N., J. Biomolec. Str. Dyn., 1986, vol. 4, pp. 391-400.
14. Trifonov, E.N., J. Biosci., Suppl., 1985, vol. 8, pp. 781-790.
15. LeStourgeon, W.M., Barnett, S.F., and Northington, S.J., The Eukaryotic Nucleus, Strauss, P.R. and Wilson, S.H., Eds., Telford, 1990, vol. 2, pp. 477-502.
16. Berman, A.L., Kolker, E., and Trifonov, E.N., Proc. Natl. Acad. Sci. USA, 1994, vol. 91, pp. 4044-4047
17. Trifonov, E.N., J. Molec. Evol., 1994, vol. 38, pp. 543-546.
18. Trifonov, E.N., J. Molec. Evol., 1985, vol. 40, pp. 337-342.
19. Kolker, E. and Trifonov, E.N., Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 557-560.
20. Gaubatz, J.W., Mut. Res., 1990, vol. 237, pp. 271-292.
21. Trifonov, E.N., J. Biomolec. Str. Dyn. (in press).
22. Wada-Kiyama, Y. and Kiyama, R., J. Biol. Chem., 1995, vol. 270, pp. 12439-12445.
23. Burgoyne, L.A. and Skinner, J.D., Biochem. Biophys. Res. Commun., 1981, vol. 99, pp. 893-899.
24. Khachatrian, A.T., Pospelov, V.A., Svetlikova, S.B., and Vorobiev, V.I., FEBS Lett., 1981, vol. 128, pp. 90-92.
25. Trifonov, E.N., Modelling of Biomolecular Structures and Mechanisms, Pullman, E., Jortner, J., and Pullman, B., Eds., Kluwer, 1995, pp. 473-479.
26. Kabsch, W., Sander, C., and Trifonov, E.N., Nucleic Acids Res., 1982, vol. 10, pp. 1097-1104.
27. van Holde, K.E., Chromatin, Springer, 1988.
28. Ponder, B.A.J. and Crawford, L.V., Cell, 1977, vol. 11, pp. 35-49.
29. Chao, M.V., Gralla, J., and Martinson, G., Biochemistry, 1979, vol. 18, pp. 1088-1094.
30. Ioshikhes, I. and Trifonov, E.N., Nucleic Acids Res., 1993, vol. 21, pp. 4857-4859.
31. Trifonov, E.N. and Sussman, J.L., Proc. Natl. Acad. Sci. USA, 1980, vol. 77, pp. 3816-3820.
32. Trifonov, E.N., Nucleic Acids Res., 1980, vol. 8, pp. 4041-4053.
33. Mengeritsky, G. and Trifonov, E.N., Nucleic Acids Res., 1983, vol. 11, pp. 3833-3851.
34. Ioshikhes, I., Bolshoy, A., and Trifonov, E.N., J. Biomolec. Str. Dyn., 1992, vol. 9, pp. 1111-1117.
35. Ioshikhes, I., Bolshoy, A., Derenshteyn, K., Borodovsky, M., and Trifonov, E.N., J. Mol. Biol., 1996, vol. 262, pp. 129-139.
36. Satchwell, S., Drew, H.R., and Travers, A.A., J. Mol. Biol., 1986, vol. 191, pp. 659-675.
37. Staffelbach, H., Koller, T., and Burks, C , J. Biomolec. Str. Dyn., 1994, vol. 12, pp. 301-325.
38. Bolshoy, A., Nature Struct. Biol., 1995, vol. 2, pp. 446-448.
39. Creighton, T.E., Proteins: Structure and Molecular Properties, Freeman, 1993, 2nd ed.
40. Matthews, B.W., Jansonius, J.N., Colman, P.M., Schoenborn, B.P., and Dupourque, D., Nature New Biol., 1972, vol. 238, pp. 37-41.
41. Jacobson, R.H., Zhang, X.-J., Dubose, R.F., and Matthews, B.W., Nature, 1994, vol. 369, pp. 761-766.
42. Orengo, C.A., Jones, D.T., and Thornton, J.M., Nature, 1994, vol. 372, pp. 631-634.
43. Russell, R.B. and Barton, G.J., J. Mol. Biol., 1994, vol. 244, pp. 332-350.
44. Kolker, E. and Trifonov, E.N., Biological Structure and Dynamics, Sarma, R.H. and Sarma, M.H., Eds., Adenine Press, 1996, pp. 257-266.
45. Breathnach, R. and Chambon, P., Annu. Rev. Biochem., 1981, vol. 50, pp. 349-383.
46. Mount, S.M., Nucleic Acids Res., 1982, vol. 10, pp. 459-472.
47. Gilbert, W., Nature, 1978, vol. 271, p. 501.
48. Zuckerkandl, E., Molec. Biol. Rep., 1981, vol. 7, pp. 149-158.
49. Stoltzfus, A., Spencer, D.F., Zuker, M., Logsdon, J.M., and Doolittle, W.F., Science, 1995, vol. 268, pp. 1367-1369.
50. Long, M., Rosenberg, C., and Gilbert, W., Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 12495-12499.
51. Beckmann, J.S. and Trifonov, E.N., Proc. Natl. Acad. Sci. USA, 1991, vol. 88, pp. 2380-2383.
52. Soloviev, V.V. and Kolchanov, N.A., Doklady Biochem., 1986, vol. 284, pp. 286-290.
53. Liu, K., Sandgren, E.P., Palmiter, R.D., and Stein, A., Proc. Natl Acad. Sci. USA, 1995, vol. 92, pp. 7724-7728.
54. Felsenfeld, G., Nature, 1992, vol. 355, pp. 219-224.
55. Goldberg, M., PhD Thesis, Stanford: Stanford Univ., 1979.
56. Carra, J.H. and Schleif, R.F., EMBO J., 1993, vol. 12, pp. 35-44.
57. Bolshoy, A., McNamara, P., Harrington, R.E., and Trifonov, E.N., Proc. Natl. Acad. Sci USA, 1991, vol. 88, pp. 2312-2316.
58. Gorin, A.A., Zhurkin, V.B., and Olson, W.K., J. Mol. Biol., 1995, vol. 247, pp. 34-48.
59. De Santis, P., Palleschi, A., Savino, M., and Scipioni, A., Biochemistry, 1990, vol. 29, pp. 9269-9273.
60. Lavery, R. and Hartmann, B., Biophys. Chem., 1994, vol. 50, pp. 33-45.
61. Nassar, R.F. and Cook, R.D., Genet. Res., 1976, vol. 27, pp. 353-362.
62. Trifonov, E.N., J. Mol. Biol., 1987, vol. 194, pp. 643-652.
63. Curran, J.F. and Gross, B.L., J. Mol. Biol., 1994, vol. 235, pp. 389-395.
64. D'Onofrio, G. and Bernardi, G., Gene, 1992, vol. 110, pp. 81-88.
65. Maslov, D.A., Avila, H.A., Lake, J.A., and Simpson, L., Nature, 1994, vol. 368, pp. 345-348.
66. Kurland, C.G., FEBS Lett., 1991, vol. 285, pp. 165-169.
67. Shpaer, E.G., Nucleic Acids Res., 1985, vol. 13, pp. 275-288.
68. Varshavsky, A., Cell, 1992, vol. 69, pp. 725-735.
69. Minchenkova, L.E., Schyolkina, A.K., Chernov, B.K., and Ivanov, V.I., J. Biomolec. Str. Dyn., 1986, vol. 4, pp. 463-476.
70. Basham, B., Schroth, G.P., and Ho, P.S. Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 6464-6468.
71. Trifonov, E.N., Advances in Biomolecular Simulations. AIP Conf. Proc., Lavery, R., Rivail, J.-L., and Smith, J., Eds., AIP, 1991, pp. 329-338.
72. Trifonov, E.N., Structure and Methods, vol. 1, Human Genome Initiative and DNA Recombination, Sarma, R.H. and Sarma, M.H., Eds., Adenine Press, 1990, pp. 69-77.
73. Normark, S., Bergstrom, S., Edlund, T., Grundstrom, T., Jaurin, B., Lindberg, F.P., and Olsson, O., Annu. Rev. Genet., 1983, vol. 17, pp. 499-525.
74. Popov, O., Segal, D.M., and Trifonov, E.N., BioSystems, 1996, vol. 38, pp. 65-74.