Abstract
Ribosomal frameshifting at a particular site can yield two protein products from one coding sequence or one protein product from two overlapping open reading frames. Many organisms are known to utilize ribosomal frameshifting to express a minority of genes. However, finding ribosomal frameshift sites by a computational method is difficult because frameshift signals are diverse and dependent on the organisms and environments. There are few computer programs available for public use to identify frameshift sites from genomic sequences. We have developed a web-based application program called FSFinder2 for predicting frameshift sites of general type. We tested FSFinder2 on the Escherichia coli K12 genome to detect potential -1 frameshifting genes. From the genome sequence, we identified 18,401 frameshift sites following the X XXY YYZ motif. 11,530 frameshift sites out of the 18,401 sites include secondary structures. Comparison with the GenBank annotation produced 11 potential frameshift sites, including 3 known frameshift sites. The program is useful for analyzing frameshifts of various types and for discovering new genes expressed by frameshifts.
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References
Farabaugh, P.J.: Programmed Translational Frameshifting. Ann. Rev. Genetics 30, 507–528 (1996)
Gesteland, R.F., Atkins, J.F.: Recoding: Dynamic Reprogramming of Translation. Annu. Rev. Biochem. 65, 741–768 (1996)
Herr, A.J., Gesteland, R.F., Atkins, J.F.: One Protein From Two Open Reading Frames: Mechanism of a 50 ntTranslational Bypass. EMBO J. 19, 2671–2680 (2000)
Baranov, P.V., Gesteland, R.F., Atkins, J.F.: Recoding: Translational Bifurcations in Gene Expression. Gene 286, 187–201 (2002)
Moon, S., Byun, Y., Kim, H.-J., Jeong, S., Han, K.: Predicting Genes Expressed via -1 and +1 Frameshifts. Nucleic Acids Research 32, 4884–4892 (2004)
Bekaert, M., Bidou, L., Denise, A., Duchateau-Nguyen, G., Forest, J., Froidevaux, C., Hatin, R.J., Termier, M.: Towards a Computational Model for -1 Eukaryotic Frameshifting Sites. Bioinformatics 19, 327–335 (2003)
Hammell, A.B., Taylor, R.C., Peltz, S.W., Dinman, J.D.: Identification of Putative Programmed -1 Ribosomal Frameshift Signals in Large DNA Databases. Genome Research 9, 417–427 (1999)
Ramos, F.D., Carrasco, M., Doyle, T., Brierley, I.: Programmed -1 Ribosomal Frameshifting in the SARS Coronavirus. Biochemical Society Transactions 32, 1081–1083 (2004)
Shah, A.A., Giddings, M.C., Parvaz, J.B., Gesteland, R.F., Atkins, J.F., Ivanov, I.P.: Computational Identification of Putative Programmed Translational Frameshift Sites. Bioinformatics 18, 1046–1053 (2002)
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© 2006 Springer-Verlag Berlin Heidelberg
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Moon, S., Byun, Y., Han, K. (2006). Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome. In: Huang, DS., Li, K., Irwin, G.W. (eds) Computational Intelligence and Bioinformatics. ICIC 2006. Lecture Notes in Computer Science(), vol 4115. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11816102_65
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DOI: https://doi.org/10.1007/11816102_65
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