Abstract
A fast genetic algorithm GArna for mass calculations of RNA secondary structures through the Internet is proposed. The algorithm GArna was used to study the effects of nucleotide composition on characteristics of the secondary structure of random RNA sequences. A contextual characteristics for evaluation of the stability was proposed and the application of standard statistical tests for heterogeneous RNA samplings was justified. The structure-contextual characteristics by which the 5"-untranslated regions of high- and low-expression genes of dicot plants and mammals differ were found, and the results were interpreted in terms of secondary structure influence on translation initiation and on the general scheme of expression regulation. The application of the results obtained for the development of computer methods for RNA structural genomics, in particular, for RNA search in genome sequences, is discussed.
Similar content being viewed by others
References
N. A. Kolchanov, I. I. Titov, I. E. Vlassova, and V. V. Vlassov, Prog. Nucl. Acids Res. Mol. Biol., 1996, 53, 196.
M. Zuker, Curr. Opin. Struct. Biol., 2000, 10, 303.
D. F. Mathews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol., 1999, 288, 911.
J. McCaskill, Biopolymers, 1990, 29, 1105.
A. A. Mironov and A. E. Kister, J. Biomol. Struct. Dyn., 1986, 4, 1.
A. Fernandez, Phys. Rev. (E), 1993, 48, 3107.
H. Ogata, Y. Akiyama, and M. Kanehisa, Nucl. Acids Res., 1995, 23, 419.
A. P. Gultyaev, F. H. D. van Batenburg, and C. W. A. Pleij, J. Mol. Biol., 1995, 250, 37.
G. Benedetti and S. Morosetti, Biophys. Chem., 1995, 55, 253.
K. M. Currey and B. A. Shapiro, Comput. Applic. Biosci., 1997, 13, 1.
V. Proutski, E. A. Gould, and E. C. Holmes, Nucl. Acids Res., 1997, 25, 1194.
I. I. Titov, V. A. Ivanisenko, and N. A. Kolchanov, Comput. Techn., 2000, 5, 48.
S. Forrest, Science, 1993, 261, 872.
D. Goldberg, Genetic Algorithms in Search, Optimization, and Machine Learning, Addison-Wesley, San Mateo, CA, 1989.
J. A. Jaeger, D. H. Turner, and M. Zuker, Proc. Natl. Acad. Sci. USA, 1989, 86, 7706.
A. V. Kochetov, M. P. Ponomarenko, A. S. Frolov, L. L. Kisselev, and N. A. Kolchanov, Bioinformatics, 1999, 15, 704.
E. Wingender, X. Chen, R. Hehl, H. Karas, I. Liebich, V. Matys, T. Meinhardt, M. Pruss, I. Reuter, and F. Schacherer, Nucl. Acids Res., 2000, 28, 316.
R. V. Davuluri, Y. Suzuki, S. Sugano, and M. Q. Zhang, Genome Res., 2000, 10, 1807.
J. P. Abrahams, M. van den Berg, E. van Batenburg, and C. W. A. Pleij, Nucl. Acids Res., 1990, 18, 3035.
W. Fontana, D. A. M. Konnings, P. F. Stadler, and P. Schuster, Biopolymers, 1993, 33, 1389.
N. Wirth, Algorithms and Data Structure, New Jersey 07632, Prentice-Hall, Inc., Englewood Cliffs, 1986.
B. A. Shapiro, Comput. Applic. Biosci., 1988, 4, 387.
M. Zuker and D. Sankoff, Bull. Math. Biol., 1984, 46, 591.
W. Fontana, T. Griesmacher, W. Schnabl, P. F. Stadler, and P. Schuster, Monatsh. Chemie, 1991, 122, 795.
H. M. Martinez, Nucl. Acids Res., 1984, 12, 323.
R. Nussinov and G. Pieczenik, J. Theor. Biol., 1984, 106, 244.
E. Rivas and S. R. Eddy, Bioinformatics, 2000, 16, 583.
S. Y. Le and J. V. Maizel, Nucl. Acids Res., 1997, 25, 362.
W. Seffens and D. Digby, Nucl. Acids Res., 1999, 27, 1578.
P. G. Higgs, J. Phys. I. France, 1993, 3, 43.
M. Kozak, Biochimie, 1994, 76, 815.
G. Bernardi and G. Bernardi, J. Mol. Evol., 1986, 24, 1.
G. Bernardi, Gene, 2000, 241, 3.
I. I. Titov, D. G. Vorobiev, and N. A. Kolchanov, Intern. Conf. on Bioinformatics of Genome Regulation and Structure BGRS-2000 (Novosibirsk, August 7-11, 2000), Novosibirsk, 2000, 138.
H. Caron, B. van Schaik, M. van der Mee, F. Baas, G. Riggins, P. van Sluis, M.-C. Hermus, R. van Asperen, K. Boon, P. A. Voute, S. Heisterkamp, A. van Kampen, and R. Versteeg, Science, 2001, 291, 1289.
V. Bourdeau, G. Ferbeyre, M. Pageau, B. Paquin, and R. Cedergren, Nucleic Acids Res., 1999, 27, 4457.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Titov, I.I., Vorobiev, D.G., Ivanisenko, V.A. et al. A fast genetic algorithm for RNA secondary structure analysis. Russian Chemical Bulletin 51, 1135–1144 (2002). https://doi.org/10.1023/A:1020945806836
Issue Date:
DOI: https://doi.org/10.1023/A:1020945806836