Prediction of Ribosomal -1 Frameshifts in the Escherichia coli K12 Genome

  • Sanghoon Moon
  • Yanga Byun
  • Kyungsook Han
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4115)


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.


Ribosomal Frameshift Translational Frameshift Frameshift Site Slippery Sequence Frameshift Event 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Farabaugh, P.J.: Programmed Translational Frameshifting. Ann. Rev. Genetics 30, 507–528 (1996)CrossRefGoogle Scholar
  2. 2.
    Gesteland, R.F., Atkins, J.F.: Recoding: Dynamic Reprogramming of Translation. Annu. Rev. Biochem. 65, 741–768 (1996)CrossRefGoogle Scholar
  3. 3.
    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)CrossRefGoogle Scholar
  4. 4.
    Baranov, P.V., Gesteland, R.F., Atkins, J.F.: Recoding: Translational Bifurcations in Gene Expression. Gene 286, 187–201 (2002)CrossRefGoogle Scholar
  5. 5.
    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)CrossRefGoogle Scholar
  6. 6.
    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)CrossRefGoogle Scholar
  7. 7.
    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)Google Scholar
  8. 8.
    Ramos, F.D., Carrasco, M., Doyle, T., Brierley, I.: Programmed -1 Ribosomal Frameshifting in the SARS Coronavirus. Biochemical Society Transactions 32, 1081–1083 (2004)CrossRefGoogle Scholar
  9. 9.
    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)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Sanghoon Moon
    • 1
  • Yanga Byun
    • 1
  • Kyungsook Han
    • 1
  1. 1.School of Computer Science and EngineeringInha UniversityInchonKorea

Personalised recommendations