ArticleBMC bioinformatics2008
RNA STRAND: the RNA secondary structure and statistical analysis database.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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Who cites it
123 citing papers in PubMed.
- The Use of Deep Learning in RNA Therapeutic Development.ACS nano · 2026Review
- Spark: sparse hierarchical energy minimization for scalable prediction of RNA pseudoknots.Bioinformatics (Oxford, England) · 2026Article
- Machine learning for RNA secondary structure prediction: a review of current methods and challenges.RNA (New York, N.Y.) · 2026Review
- Hierarchical analysis of RNA secondary structures with pseudoknots based on sections.PLoS computational biology · 2026Article
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- CParty: hierarchically constrained partition function of RNA pseudoknots.Bioinformatics (Oxford, England) · 2024Article
- Predicting RNA sequence-structure likelihood via structure-aware deep learning.BMC bioinformatics · 2024Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration.Algorithms for molecular biology : AMB · 2024Article
- Multiple sequence alignment-based RNA language model and its application to structural inference.Nucleic acids research · 2024Article
- Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.Algorithms for molecular biology : AMB · 2023Article
- Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery.Briefings in bioinformatics · 2023Review
- Machine learning for RNA 2D structure prediction benchmarked on experimental data.Briefings in bioinformatics · 2023Review
- bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures.RNA (New York, N.Y.) · 2023Article
- RNA independent fragment partition method based on deep learning for RNA secondary structure prediction.Scientific reports · 2023Article
- DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.Nucleic acids research · 2023Article
- Article
- Deep learning models for RNA secondary structure prediction (probably) do not generalize across families.Bioinformatics (Oxford, England) · 2022Article
- RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform.PLoS computational biology · 2022Article
- Prediction of RNA secondary structure including pseudoknots for long sequences.Briefings in bioinformatics · 2022Article
63 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures.
resultsIn this paper we describe RNA STRAND - the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND.
conclusionRNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.
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