Summary
The nucleotide sequence of the RNA of the bacteriophage MS2 was examined by computer for internal patterns. We used a technique which analyzes a nucleotide sequence as a Markov chain. This led us to discover patterns within the translated and untranslated regions of the RNA in addition to those patterns formed by the codons. One of the more surprising results of this analysis was the discovery that the non-coding sequences in the genome are as highly ordered, although in a different sense, as the genes themselves. Also of interest was the discovery that the codon frequency distributions for the three genes are similar.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Barucha-Reid, A. S.: Elements of the Theory of Markov Processes and Their Applications, New York: McGraw-Hill, 1960
Berger, E. M.: Pattern and chance in the use of the genetic code. J. Mol. Evol. 10, 319–323 (1978)
De Wachter, R., Merregaert, J., Vandenberghe, A., Contreras, R., Fiers, W.: Studies on the bacteriophage MS2: The untranslated 5′-terminal nucleotide sequence proceeding the first cistron. Eur. J. Biochem. 22, 400–414 (1971)
Engelberg, H., Schoulaker, R.: Sequence homologies between ribosomal and phage RNA: A proposed molecular basis for RNA phage parasitism. J. Mol. Biol. 106, 709–733 (1976)
Fiers, W., Contreras, R., Duerinck, F., Haegeman, G., Merregaert, J., Min Jou, W., Raeymaekers, A., Volckaert, G., Ysebaert, M., Van de Kerckhove, J., Nolf, F., Van Montagu, M.: A-protein gene of bacteriophage MS2. Nature (London) 256, 273–278 (1975)
Fiers, W., Contreras, R., Duerinck, R., Haegeman, G., Iserentant, D., Merregaert, J., Min Jou, W., Molemans, F., Raeymaekers, A., Vandenberghe, A., Volckaert, G., Ysebaert, M.: Complete nucleotide sequence of bacteriophage MS2: Primary and secondary structure of the replicase gene. Nature (London) 260, 500–507 (1976)
Kullback, S., Kupperman, M., Ku, H. H.: Tests for contingency tables and Markov chains. Technometrics 4, 573–608 (1962)
Low, B. L., Lovell, F. M., Rudko, A. D.: Prediction of α-helical regions in proteins of known sequence. Proc. Natl. Acad. Sci. USA 60, 1519–1526 (1968)
Min Jou, W., Fiers, W.: Studies on bacteriophage MS2: XXXIII. Comparison of the nucleotide sequences in related bacteriophage RNAs. J. Mol. Biol. 106, 1047–1060 (1976)
Min Jou, W., Haegeman, G., Ysebaert, M., Fiers, W.: Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein. Nature (London) 237, 82–88 (1972)
Sanger, F., Air, G. M., Barrell, B. G., Brown, N. L., Coulson, A. R., Fiddes, J. C., Hutchison, C. A. III, Slocombe, P. M., Smith, M.: Nucleotide sequence of bacteriophage φX174 DNA. Nature (London) 265, 687–695 (1977)
Sankoff, D., Cedergren, R. J.: A test for nucleotide sequence homology. J. Mol. Biol. 77, 159–164 (1973)
Vandenberghe, A., Min Jou, W., Fiers, W.: 3′-terminal nucleotide sequence (n=361) of bacteriophage MS2 RNA. Proc. Nat. Acad. Sci. U.S.A. 72, 2559–2562 (1975)
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Erickson, J.W., Altman, G.G. A search for patterns in the nucleotide sequence of the MS2 genome. J. Math. Biology 7, 219–230 (1979). https://doi.org/10.1007/BF00275725
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF00275725