 |
|
| HAL: hal-00641738, version 1 |
| DOI: 10.1016 |
| See detailed view |  BibTeX,EndNote,... |
 |
| Computational Biology and Chemistry 37 (2012) 1-5 |
|
|
|
|
| Automated prediction of three-way junction topological families in RNA secondary structures |
|
|
| Alexis Lamiable 1, 2Dominique Barth 1 |
|
|
| (2012-01-11) |
|
|
|
| We present an algorithm for automatically predicting the topological family of any RNA three-way junction, given only the information from the secondary structure: the sequence and the Watson-Crick pairings. The parameters of the algorithm have been determined on a data set of 33 three-way junctions whose 3D conformation is known. We applied the algorithm on 53 other junctions and compared the predictions to the real shape of those junctions. We show that the correct answer is selected out of nine possible con gurations 64 % of the time. Additionally, these results are noticeably improved if homology information is used. The resulting software, Cartaj, is available online and downloadable (with source) at: http://cartaj.lri.fr |
|
|
|
|
|
|
|
|
|
|
|
| 1: | Parallélisme, Réseaux, Systèmes d'information, Modélisation (PRISM) |
|
|
|
CNRS : UMR8144 – Université de Versailles Saint-Quentin-en-Yvelines |
|
|
| 2: | Laboratoire de Recherche en Informatique (LRI) |
|
|
|
CNRS : UMR8623 – Université Paris XI - Paris Sud |
|
|
| 3: | AMIB (INRIA Saclay - Ile de France) |
|
|
|
INRIA – Polytechnique - X – CNRS : UMR8623 – Université Paris XI - Paris Sud |
|
|
| 4: | Institut de génétique et microbiologie (IGM) |
|
|
|
CNRS : UMR8621 – Université Paris XI - Paris Sud |
|
|
| 5: | Architecture et réactivité de l'ARN (ARN) |
|
|
|
CNRS : UPR9002 – Université de Strasbourg |
|
|
|
|
|
|
|
|
|
| Domain | : | Computer Science/Bioinformatics Life Sciences/Quantitative Methods |
| hal-00641738, version 1 | |
| http://hal.inria.fr/hal-00641738 | |
| oai:hal.inria.fr:hal-00641738 | |
| From: Alain Denise | |
| Submitted on: Wednesday, 16 November 2011 15:17:28 | |
| Updated on: Friday, 10 February 2012 08:53:48 | |
