Abstract
Nucleic acid sequences may be looked upon as words over the alphabet of nucleotides. Naturally occurring DNAs and RNAs form subsets of the set of all possible words. The use of formal languages is proposed to describe the structure of these subsets. Regular languages defined by finite automata are introduced to demonstrate the application of the concept on RNA-phages of group I. This approach permits a concise characterization of grammatical patterns in genetic information.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Abelson J. RNA processing and the intervening sequence problem. Annu Rev Biochem. 1979;48:1035–1069. doi: 10.1146/annurev.bi.48.070179.005131. [DOI] [PubMed] [Google Scholar]
- Crick F. H. The genetic code. 3. Sci Am. 1966 Oct;215(4):55–passim. doi: 10.1038/scientificamerican1066-55. [DOI] [PubMed] [Google Scholar]
- Grunberg-Manago M., Gros F. Initiation mechanisms of protein syntehesis. Prog Nucleic Acid Res Mol Biol. 1977;20:209–284. doi: 10.1016/s0079-6603(08)60474-2. [DOI] [PubMed] [Google Scholar]
- Kastelein R. A., Remaut E., Fiers W., van Duin J. Lysis gene expression of RNA phage MS2 depends on a frameshift during translation of the overlapping coat protein gene. Nature. 1982 Jan 7;295(5844):35–41. doi: 10.1038/295035a0. [DOI] [PubMed] [Google Scholar]
- Lindenmayer A. Developmental systems without cellular interactions, their languages and grammars. J Theor Biol. 1971 Mar;30(3):455–484. doi: 10.1016/0022-5193(71)90002-6. [DOI] [PubMed] [Google Scholar]
- Martinez H. M. An automaton analogue of unicellularity. Biosystems. 1979 Aug;11(2-3):133–162. doi: 10.1016/0303-2647(79)90007-8. [DOI] [PubMed] [Google Scholar]
- Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sanger F., Coulson A. R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975 May 25;94(3):441–448. doi: 10.1016/0022-2836(75)90213-2. [DOI] [PubMed] [Google Scholar]
- Shapiro B. Language processor generation with BNF inputs: methods and implementation. Comput Programs Biomed. 1977 Jun;7(2):85–98. doi: 10.1016/0010-468x(77)90015-0. [DOI] [PubMed] [Google Scholar]
- Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weissmann C., Billeter M. A., Goodman H. M., Hindley J., Weber H. Structure and function of phage RNA. Annu Rev Biochem. 1973;42:303–328. doi: 10.1146/annurev.bi.42.070173.001511. [DOI] [PubMed] [Google Scholar]