Computational Identification of -1 Frameshift Signals

  • Sanghoon Moon
  • Yanga Byun
  • Kyungsook Han
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3036)


Ribosomal frameshifts in the -1 direction are used frequently by RNA viruses to synthesize a single fusion protein from two or more overlapping open reading frames. The slippery heptamer sequence XXX YYY Z is the best recognized of the signals that promote -1 frameshifting. We have developed an algorithm that predicts plausible -1 frameshift signals in long DNA sequences. Our algorithm is implemented in a working program called FSFinder (Frameshift Signal Finder). We tested FSFinder on 72 genomic sequences from a number of organisms and found that FSFinder predicts -1 frameshift signals efficiently and with greater sensitivity and selectivity than existing approaches. Sensitivity is improved by considering all potentially relevant components of frameshift signals, and selectivity is increased by focusing on overlapping regions of open reading frames and by prioritizing candidate frameshift signals. FSFinder is useful for analyzing -1 frameshift signals as well as discovering unknown genes.


Mouse Mammary Tumor Virus Computational Identification Rous Sarcoma Virus Nucleic Acid Research Ribosomal Frameshift 
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.


  1. 1.
    Vimaladithan, A., Farabaugh, P.J.: Identification and analysis of frameshift sites. Methods in Molecular Biology 77, 399–411 (1998)Google Scholar
  2. 2.
    Farabaugh, P.J.: Programmed translational frameshifting. Microbiological Reviews 60, 103–134 (1996)Google Scholar
  3. 3.
    Farabaugh, P.J.: Programmed translational frameshifting. Annual Review of Genetics 30, 507–528 (1996)CrossRefGoogle Scholar
  4. 4.
    Jacks, T., Varmus, H.E.: Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting. Science 230, 1237–1242 (1985)CrossRefGoogle Scholar
  5. 5.
    Bekaert, M., Bidou, L., Denise, A., Duchateau-Nguyen, G., Forest, J., Froidevaux, C., Hatin, I., Rousset, J., Termier, M.: Towards a computational model for -1 eukaryotic frameshifting sites. Bioinformatics 19, 327–335 (2003)CrossRefGoogle Scholar
  6. 6.
    Dinman, J.D., Icho, T., Wickner, R.B.: A -1 ribosomal frameshift in a double-stranded RNA virus of yeast forms a gag-pol fusion protein. Proc. Natl. Acad. Sci. USA 88, 174–178 (1991)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 Res. 9, 417–427 (1999)Google Scholar
  8. 8.
    Marck, C.: DNA Strider: a C program for the fast analysis of DNA and protein sequence on the Apple Macintosh family of computers. Nucleic Acids Research 16, 1829–1836 (1988)CrossRefGoogle Scholar
  9. 9.
    van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A., Ng, J., Oliehoek, J.: PseudoBase: a database with RNA pseudoknots. Nucleic Acids Research 28, 201–204 (2000)CrossRefGoogle Scholar
  10. 10.
    Baranov, P., Gurvich, O.L., Hammer, A.W., Gesteland, R.F., Atkins, J.F.: RECODE. Nucleic Acids Research 31, 87–89 (2003)Google Scholar
  11. 11.
    Birney, E., Thompson, J.D., Gibson, T.J.: PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Research 24, 2730–2739 (1996)CrossRefGoogle Scholar
  12. 12.
    Halperin, E., Faigler, S., Gill-More, R.: FramePlus: aligning DNA to protein sequences. Bioinformatics 15, 867–873 (1999)CrossRefGoogle Scholar
  13. 13.
    Fichant, G.A., Quentin, Y.: A frameshift error detection algorithm for DNA sequencing projects. Nucleic Acids Research 23, 2900–2908 (1995)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

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

Personalised recommendations