title: Towards a computational model for -1 eukaryotic frameshifting sites.
abstract: 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/.
authors.affiliation: Génétique Moléculaire de la Traduction, UMR CNRS 8623, Université Paris-Sud, 91405 Orsay Cedex, France. bekaert@igmors.u-psud.fr
authors.forename: Michaël
authors.initials: M
authors.lastname: Bekaert
authors.forename: Laure
authors.initials: L
authors.lastname: Bidou
authors.forename: Alain
authors.initials: A
authors.lastname: Denise
authors.forename: Guillemette
authors.initials: G
authors.lastname: Duchateau-Nguyen
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Forest
authors.forename: Christine
authors.initials: C
authors.lastname: Froidevaux
authors.forename: Isabelle
authors.initials: I
authors.lastname: Hatin
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Rousset
authors.forename: Michel
authors.initials: M
authors.lastname: Termier
mesh_terms: 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*
chemical_list: D021903:DNA, Ribosomal Spacer