ArticleBMC bioinformatics2010
RNAstructure: software for RNA secondary structure prediction and analysis.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,169 papers.
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Who cites it
1,169 citing papers in PubMed.
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- Markov models of SHAPE data improve secondary structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Nearest Neighbor Parameters for Estimating RNA Folding Stability withbioRxiv : the preprint server for biology · 2026Article
- Modified Plasmids and Inverted Terminal Repeats Enhance Adeno-Associated Virus Production and Performance.International journal of molecular sciences · 2026Article
- Article
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- Reduced sensitivity to RNA structural differences distinguishes eukaryotic Pus4 from bacterial TruB.RNA (New York, N.Y.) · 2026Article
- Folding the message: mRNA structure as a regulatory layer of human mitochondrial gene expression.Biochimica et biophysica acta. Molecular cell research · 2026Review
- DMS-MaPseq and DREEM Analyses Implicate the Critical Role of RNA Structural Dynamics in Turnip Yellow Mosaic Virus Pathogenicity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Cross-genus analysis reveals architecturally programmed sgRNA synthesis patterns in coronaviruses.Molecular systems biology · 2026Article
- ShapeRNA: an integrated web server for RNA secondary structure, ensemble, and functional analysis.Nucleic acids research · 2026Article
- Identification of the SARS-CoV-2 genome packaging signal in the nsp12-coding region.Nature communications · 2026Article
- A nitrite-responsive regulatory RNA locus sustains commensal resilience against nitrosative stress.bioRxiv : the preprint server for biology · 2026Article
- Phylogenetic Inference and Ancestral Character Reconstruction of Diphyllobothriid Tapeworms (Cestoda: Diphyllobothriidae).Animals : an open access journal from MDPI · 2026Article
- Human RPL7 and DDX21 function synergistically with HTLV-1 Gag to overcome genomic RNA structural barriers that block tRNAPro primer annealing.Nucleic acids research · 2026Article
1,109 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundTo understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.
resultsRNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.
conclusionThe extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.
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Registered trials
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