BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

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...

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Detalles Bibliográficos
Autores principales: Allali, Julien, Saule, Cédric, Chauve, Cédric, d'Aubenton-Carafa, Yves, Denise, Alain, Drevet, Christine, Ferraro, Pascal, Gautheret, Daniel, Herrbach, Claire, Leclerc, Fabrice, de Monte, Antoine, Ouangraoua, Aida, Sagot, Marie-France, Termier, Michel, Thermes, Claude, Touzet, Hélène
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2012
Materias:
Resource Review
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366197/
https://www.ncbi.nlm.nih.gov/pubmed/22675348
http://dx.doi.org/10.1155/2012/893048
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author Allali, Julien
Saule, Cédric
Chauve, Cédric
d'Aubenton-Carafa, Yves
Denise, Alain
Drevet, Christine
Ferraro, Pascal
Gautheret, Daniel
Herrbach, Claire
Leclerc, Fabrice
de Monte, Antoine
Ouangraoua, Aida
Sagot, Marie-France
Termier, Michel
Thermes, Claude
Touzet, Hélène
author_facet Allali, Julien
Saule, Cédric
Chauve, Cédric
d'Aubenton-Carafa, Yves
Denise, Alain
Drevet, Christine
Ferraro, Pascal
Gautheret, Daniel
Herrbach, Claire
Leclerc, Fabrice
de Monte, Antoine
Ouangraoua, Aida
Sagot, Marie-France
Termier, Michel
Thermes, Claude
Touzet, Hélène
author_sort Allali, Julien
collection PubMed
description 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.
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spelling pubmed-33661972012-06-06 BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms Allali, Julien Saule, Cédric Chauve, Cédric d'Aubenton-Carafa, Yves Denise, Alain Drevet, Christine Ferraro, Pascal Gautheret, Daniel Herrbach, Claire Leclerc, Fabrice de Monte, Antoine Ouangraoua, Aida Sagot, Marie-France Termier, Michel Thermes, Claude Touzet, Hélène Adv Bioinformatics Resource Review 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. Hindawi Publishing Corporation 2012 2012-05-23 /pmc/articles/PMC3366197/ /pubmed/22675348 http://dx.doi.org/10.1155/2012/893048 Text en Copyright © 2012 Julien Allali et al. https://creativecommons.org/licenses/by/3.0/ 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.
spellingShingle Resource Review
Allali, Julien
Saule, Cédric
Chauve, Cédric
d'Aubenton-Carafa, Yves
Denise, Alain
Drevet, Christine
Ferraro, Pascal
Gautheret, Daniel
Herrbach, Claire
Leclerc, Fabrice
de Monte, Antoine
Ouangraoua, Aida
Sagot, Marie-France
Termier, Michel
Thermes, Claude
Touzet, Hélène
BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms
title BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms
title_full BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms
title_fullStr BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms
title_full_unstemmed BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms
title_short BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms
title_sort brasero: a resource for benchmarking rna secondary structure comparison algorithms
topic Resource Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366197/
https://www.ncbi.nlm.nih.gov/pubmed/22675348
http://dx.doi.org/10.1155/2012/893048
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