Towards a computational model for -1 eukaryotic frameshifting sites.

Full Abstract

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/.

Learn Faster Today Improve your study skills

Author information

Author/s: Bekaert, Michaël (M); 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);

Affiliation: Génétique Moléculaire de la Traduction, UMR CNRS 8623, Université Paris-Sud, 91405 Orsay Cedex, France. bekaert@igmors.u-psud.fr

Journal and publication information

Publication Type: Evaluation Studies; Journal Article; Research Support, Non-U.S. Gov't; Validation Studies

Journal: Bioinformatics (Oxford, England) (Bioinformatics), published in England. (Language: eng)

Reference: 2003-Feb; vol 19 (issue 3) : pp 327-35

Dates: Created 2003/02/13; Completed 2003/06/06; Revised 2006/11/15;

PMID: 12584117, status: MEDLINE (last retrieval date: 11/6/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

External Links for this article (including full text providers, if available):

Click Electronic Full-text Provider Links to see options for finding the electronic full text links to this article. Note there may be a subscription or fee required for access to the full text. See our FAQ for information on finding FREE full text articles.

This article may also be located in paper journal collections available in many libraries. Use the Journal and Publication Information above to find the full article.

MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Associated Chemicals: DNA, Ribosomal Spacer (0)

This article has not been indexed for related articles as yet, however you can still use the live related article search links below.

See 100+ related articles.