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1.  BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms 
Advances in Bioinformatics  2012;2012:893048.
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.
doi:10.1155/2012/893048
PMCID: PMC3366197  PMID: 22675348
2.  Counting RNA Pseudoknotted Structures 
Journal of Computational Biology  2011;18(10):1339-1351.
Abstract
In 2004, Condon and coauthors gave a hierarchical classification of exact RNA structure prediction algorithms according to the generality of structure classes that they handle. We complete this classification by adding two recent prediction algorithms. More importantly, we precisely quantify the hierarchy by giving closed or asymptotic formulas for the theoretical number of structures of given size n in all the classes but one. This allows us to assess the tradeoff between the expressiveness and the computational complexity of RNA structure prediction algorithms.
doi:10.1089/cmb.2010.0086
PMCID: PMC3179619  PMID: 21548808
algorithms; combinatorics; computational molecular biology; probability; strings
3.  VARNA: Interactive drawing and editing of the RNA secondary structure 
Bioinformatics  2009;25(15):1974-1975.
Description: VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
Features: VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments.
Availability: VARNA is a free software, released under the terms of the GPLv3.0 license and available at http://varna.lri.fr
Contact: ponty@lri.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btp250
PMCID: PMC2712331  PMID: 19398448

Results 1-3 (3)