Abstract
The translation of a messenger RNA into a functional protein is one of the most fundamental molecular processes in a cell. Groups of three ribonucleotides, called codons, uniquely specify amino acids to be used in the construction of a protein. When the translation process skips a number of bases it is possible for the reading frame of the RNA to be shifted. By making use of multiple reading frames, organisms and viruses are able to encode multiple proteins in a single gene. We propose here a formal model of these frameshifting events and investigate its basic mathematical properties and their relevance to biological systems. In addition, multiple time-efficient algorithms are created for use in the study of frameshifting. Some of these algorithms are created to work in general, for any type of frameshifting which could be found in organisms, while others are optimized for known specialized types of frameshifting.
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References
Alberts B (2007) Molecular biology of the cell, 5th edn. Garland Science, NY
Baranov PV, Gesteland RF, Atkins JF (2002) Recoding: translational bifurcations in gene expression. Gene 286:187–201
Birney E, Thompson J, Gibson T (1996) PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res 24:2730–2739
Cormen TH, Leiserson CE, Rivest RL, Stein C (2001) Introduction to algorithms, 2nd edn. The MIT Press, Cambridge, MA
Guan X, Uberbacher EC (1996) Alignments of DNA and protein sequences containing frameshift errors. Comput Appl Biosci 12(1):31–40
Holub J, Melichar B (1999) Implementation of nondeterministic finite automata for approximate pattern matching. In: Champarnaud JM, Maurel D, Ziadi D (eds) WIA ’98, Lecture Notes in Computer Science, vol 1660. Springer-Verlag, Berlin, pp 92–99
Hopcroft J, Ullman J (1979) Introduction to automata theory, languages, and computation. Addison-Wesley, Reading, MA
Horton T, Landweber L (2002) Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes. Microbiology 5(6):620–626
Huang X, Zhang J (1996) Methods for comparing a DNA sequence with a protein sequence. Comput Appl Biosci 12(6):497–506
Lind D, Marcus B (1995) An introduction to symbolic dynamics and coding. Cambridge University Press, Cambridge, NY
Lozupone C, Knight R, Landweber L (2001) The molecular basis of nuclear genetic code changes in ciliates. Curr Biol 11:65–74
Prescott D (2000) Genome gymnastics: unique modes of DNA evolution and processing in ciliates. Nat Rev Genet 1:191–198
Shehu-Xhilaga M, Crowe S, Mak J (2001) Maintenance of the gag/gag-pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity. J Virol 75:1834–1841
Stahl G, McCarty GP, Farabaugh PJ (2002) Ribosome structure: Revisiting the connection between translational accuracy and unconventional decoding. Trends Biochem Sci 27(4):178–183
Acknowledgements
This research was supported by grants from the Natural Sciences and Engineering Research Council of Canada, institutional grants of the University of Saskatchewan and the University of Western Ontario and the SHARCNET Research Chairs Program.
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Daley, M., McQuillan, I. Modelling programmed frameshifting with frameshift machines. Nat Comput 9, 239–261 (2010). https://doi.org/10.1007/s11047-009-9144-x
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DOI: https://doi.org/10.1007/s11047-009-9144-x