Towards a computational model for -1 eukaryotic frameshifting sites.
BACKGROUND
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.


BACKGROUND
Sequences of the oligonucleotides in the functional tests are available at http://www.igmors.u-psud.fr/rousset/bioinformatics/.
Bekaert
Michaël
M
Génétique Moléculaire de la Traduction, UMR CNRS 8623, Université Paris-Sud, 91405 Orsay Cedex, France. bekaert@igmors.u-psud.fr
Bidou
Laure
L
Denise
Alain
A
Duchateau-Nguyen
Guillemette
G
Forest
Jean-Paul
JP
Froidevaux
Christine
C
Hatin
Isabelle
I
Rousset
Jean-Pierre
JP
Termier
Michel
M
D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D001483:Base Sequence; D001717:Birds; D003198:Computer Simulation; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005057:Eukaryotic Cells; D018965:Frameshifting, Ribosomal / Q000235:genetics*; D005786:Gene Expression Regulation; D015967:Gene Expression Regulation, Viral; D000882:Haplorhini; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA / Q000379:methods*; D014780:Viruses / Q000235:genetics*
D021903:DNA, Ribosomal Spacer