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Bioinformatics Vol. 19 no. 3 2003
Pages 327-335
© 2003 Oxford University Press

JOBIM Paper

Towards a computational model for -1 eukaryotic frameshifting sites

Michaël Bekaert 1, Laure Bidou 1, Alain Denise 2,3, Guillemette Duchateau-Nguyen 2, Jean-Paul Forest 3, Christine Froidevaux 3,*, Isabelle Hatin 1, Jean-Pierre Rousset 1 and Michel Termier 2

1 Génétique Moléculaire de la Traduction
2 Bioinformatique des Génomes, Institut de Génétique et Microbiologie (IGM), UMR CNRS 8621
3 Laboratoire de Recherche en Informatique (LRI), UMR CNRS 8623, Université Paris-Sud, 91405 Orsay Cedex, France

Received on February 1, 2002 ; revised on June 6, 2002 ; accepted on August 27, 2002

Motivation: Unconventional decoding events are now well acknowledged, but not yet well formalized. In this study, we present a bioinformatics analysis of eukaryotic -1 frameshifting, in order to model this event.

Results: A consensus model has already been established for -1 frameshifting sites. Our purpose here is to provide new constraints which make the model more precise. We show how a machine learning approach can be used to refine the current model. We identify new properties that may be involved in frameshifting. Each of the properties found was experimentally validated. Initially, we identify features of the overall model that are to be simultaneously satisfied. We then focus on the following two components: the spacer and the slippery sequence. As a main result, we point out that the identity of the primary structure of the so-called spacer is of great importance.

Availability: Sequences of the oligonucleotides in the functional tests are available at http://www.igmors.u-psud.fr/rousset/bioinformatics/

Contact: bekaert{at}igmors.u-psud.fr jpforest{at}lri.fr chris{at}lri.fr

* To whom correspondence should be addressed.


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