Prediction of Readthroughs Based on the Statistical Analysis of Nucleotides Around Stop Codons

  • Sanghoon Moon
  • Yanga Byun
  • Kyungsook Han
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3991)


Readthrough is an unusual translational event in which a stop codon is skipped or misread as a sense codon. Translation then continues past the stop codon and results in an extended protein product. Reliable prediction of readthroughs is not easy since readthrough is in competition with standard decoding and readthroughs occur only at a tiny fraction of stop codons in the genome. We developed a program that predicts readthrough sites directly from statistical analysis of nucleotides surrounding all stop codons in genomic sequences. Experimental results of the program on 86 genome sequences showed that 80% and 100% of the actual readthrough sites were found in the top 3% and 10% prediction scores, respectively.


Stop Codon Start Codon Prediction Score Translation Termination Position Specific Score Matrix 


  1. 1.
    Gesteland, R.F., Weiss, R.B., Atkins, J.F.: Recoding: re-programmed genetic decoding. Science 257, 1640–1641 (1992)CrossRefGoogle Scholar
  2. 2.
    Gestealand, R.F., Atkins, J.F.: Recoding: dynamic reprogramming of translation. Annu. Rev. Biochem. 65, 741–768 (1996)CrossRefGoogle Scholar
  3. 3.
    Namy, O., Rousset, J., Napthine, S., Brierley, I.: Reprogrammed genetic decoding in cellular gene expression. Mol. Cell 13, 157–169 (2004)CrossRefGoogle Scholar
  4. 4.
    Poole, E.S., Brown, C.H., Tate, W.P.: The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO Journal 14, 151–158 (1995)Google Scholar
  5. 5.
    Bonetti, B., Fu, L., Moon, J., Bedwell, D.M.: The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. Journal of Molecular Biology 251, 334–345 (1995)CrossRefGoogle Scholar
  6. 6.
    Namy, O., Hatin, I., Rousset, J.: Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO reports 2, 787–793 (2001)CrossRefGoogle Scholar
  7. 7.
    Harrell, L., Melcher, U., Atkins, J.F.: Predominance of six different hexanucleotide recoding signals 3’ of read-through stop codons. Nucleic Acids Res. 30, 2011–2017 (2002)CrossRefGoogle Scholar
  8. 8.
    Namy, O., Duchateau-Ngyen, G., Rousset, J.: Translational readthrough of the PDE2 stop codon modulates cAMP levels in Saccharomyces cerevisiae. Molecular Microbiology 43, 641–652 (2002)CrossRefGoogle Scholar
  9. 9.
    Mottagui-tabar, S., Tuite, M.F., Isaksson, L.A.: The influence of 5’ codon context on translation termination in Saccharomyces cerevisiae. Eur. J. Biochem. 257, 249–254 (1998)CrossRefGoogle Scholar
  10. 10.
    Williams, I., Richardson, J., Starkey, A., Stansfield, I.: Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 32, 6605–6616 (2004)CrossRefGoogle Scholar
  11. 11.
    Namy, O., Duchateau-Nguyen, G., Hatin, I., Denmat, S.H., Termier, M., Rousset, J.: Identification of stop codon readthrough genes in Saccharomyces cerevisiae. Nucleic Acids Research 31, 2289–2296 (2003)CrossRefGoogle Scholar
  12. 12.
    Sato, M., Umeki, H., Saito, R., Kanai, A., Tomita, M.: Computational analysis of stop codon readthrough in D.melanogaster. Bioinformatics 19, 1371–1380 (2003)CrossRefGoogle Scholar
  13. 13.
    Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Rapp, B.A., Wheeler, D.L.: GenBank. Nucleic Acids Res. 30, 17–20 (2002)CrossRefGoogle Scholar
  14. 14.
    Baranov, P., Gurvich, O.L., Hammer, A.W., Gesteland, R.F., Atkins, J.F.: RECODE. Nucleic Acids Res. 31, 87–89 (2003)CrossRefGoogle Scholar
  15. 15.
    Crooks, G.E., Hon, G., Chandonia, J., Brenner, S.E.: WebLogo: A sequencer logo generator. Genome Research 14, 1188–1190 (2004)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