BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms-Reference-Cited by-同舟云学术

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Published:2012-05-23 Issue: Volume:2012 Page:1-5
ISSN:1687-8027
Container-title:Advances in Bioinformatics
language:en
Short-container-title:Advances in Bioinformatics

Author:

Allali Julien¹²,Saule Cédric³,Chauve Cédric⁴,d’Aubenton-Carafa Yves⁵,Denise Alain³⁶,Drevet Christine⁶,Ferraro Pascal¹²,Gautheret Daniel⁶,Herrbach Claire³⁶,Leclerc Fabrice⁷,de Monte Antoine⁸,Ouangraoua Aida⁸,Sagot Marie-France⁹,Termier Michel⁶,Thermes Claude⁵,Touzet Hélène⁸

Affiliation:

1. LaBRI, UMR 5800 CNRS, Université Bordeaux, 351, Cours de la Libération, 33405 Talence Cédex, France

2. The Pacific Institute for the Mathematical Sciences, University of British Columbia, CNRS UMI 3069, 200-1933 West Mall Vancouver, BC, Canada V6T 1Z2

3. LRI, UMR 8623 CNRS, Université Paris-Sud and INRIA Saclay, 91405 Orsay Cédex, France

4. Department of Mathematics, Simon Fraser University, 8888 University drive, Burnaby, BC, Canada V5A 1S6

5. Centre de Génétique Moléculaire, UPR 3404 CNRS, Avenue de la Terrasse, Bât. 26, 91198 Gif-Sur-Yvette, France

6. IGM, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay Cédex, France

7. MAEM, CNRS UMR 7567, Université Henri Poincaré, 1 Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-Les-Nancy Cédex, France

8. LIFL, CNRS UMR 8022, Université Lille 1 and INRIA, 59655 Lille Cédex, France

9. Inria Rhône-Alpes and LBBE, UMR 5558 CNRS, Université Claude Bernard, Bât. Grégor Mendel, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cédex, France

Abstract

The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO that offers tools for evaluating such software tools on real and synthetic datasets.

Funder

Agence Nationale de la Recherche

Publisher

Hindawi Limited

Subject

Computer Science Applications,Biochemistry, Genetics and Molecular Biology (miscellaneous),Biomedical Engineering

Link

http://downloads.hindawi.com/archive/2012/893048.pdf

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