ArticleBioinformatics (Oxford, England)2017
FoldAtlas: a repository for genome-wide RNA structure probing data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed, 18 citations in OpenAlex.
- Unlocking translational control of specialized metabolism in plants through 5'UTR structure.Science advances · 2026Article
- Genome-Wide RNA Secondary Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RNA G-quadruplex structure contributes to cold adaptation in plants.Nature communications · 2022Article
- RNA G-quadruplex structures exist and function in vivo in plants.Genome biology · 2020Article
- RNAProbe: a web server for normalization and analysis of RNA structure probing data.Nucleic acids research · 2020Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- Probing RNA structure in vivo.Current opinion in structural biology · 2019Review
- Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants.Molecular plant · 2018Article
- Structure and Interaction Prediction in Prokaryotic RNA Biology.Microbiology spectrum · 2018Review
- Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.Quantitative biology (Beijing, China) · 2017Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
Abstract
Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work. AVAILABILITY AND IMPLEMENTATION: The FoldAtlas website can be accessed at www.foldatlas.com Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985. CONTACT: yiliang.ding@jic.ac.uk or matthew.norris@jic.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.