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Advances in Bioinformatics
Volume 2012, Article ID 893048, 5 pages
Resource Review

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

1LaBRI, UMR 5800 CNRS, Université Bordeaux, 351, Cours de la Libération, 33405 Talence Cédex, France
2The Pacific Institute for the Mathematical Sciences, University of British Columbia, CNRS UMI 3069, 200-1933 West Mall Vancouver, BC, Canada V6T 1Z2
3LRI, UMR 8623 CNRS, Université Paris-Sud and INRIA Saclay, 91405 Orsay Cédex, France
4Department of Mathematics, Simon Fraser University, 8888 University drive, Burnaby, BC, Canada V5A 1S6
5Centre de Génétique Moléculaire, UPR 3404 CNRS, Avenue de la Terrasse, Bât. 26, 91198 Gif-Sur-Yvette, France
6IGM, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay Cédex, France
7MAEM, CNRS UMR 7567, Université Henri Poincaré, 1 Boulevard des Aiguillettes, BP 239, 54506 Vandoeuvre-Les-Nancy Cédex, France
8LIFL, CNRS UMR 8022, Université Lille 1 and INRIA, 59655 Lille Cédex, France
9Inria Rhône-Alpes and LBBE, UMR 5558 CNRS, Université Claude Bernard, Bât. Grégor Mendel, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne Cédex, France

Received 28 September 2011; Accepted 22 February 2012

Academic Editor: Alejandro Schäffer

Copyright © 2012 Julien Allali et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.