ArticleNucleic acids research2021
RASP: an atlas of transcriptome-wide RNA secondary structure probing data.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 54 citations in OpenAlex.
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- Modtector: ultra-fast modification signal mining on mapped sequencing reads.Bioinformatics (Oxford, England) · 2026Article
- Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome.Genomics, proteomics & bioinformatics · 2026Article
- MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics.Genomics, proteomics & bioinformatics · 2026Article
- RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.NAR genomics and bioinformatics · 2026Article
- The role of low-complexity repeats in RNA-RNA interactions and a deep learning framework for duplex prediction.Nature communications · 2026Article
- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Consistent features observed in structural probing data of eukaryotic RNAs.NAR genomics and bioinformatics · 2025Article
- Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity.Nature structural & molecular biology · 2025Article
- ALS-associated FUS mutation reshapes the RNA and protein composition of stress granules.Nucleic acids research · 2024Article
- Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution.Nature communications · 2024Article
- Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression.Molecular systems biology · 2024Article
- PRMD: an integrated database for plant RNA modifications.Nucleic acids research · 2024Article
- Limits of experimental evidence in RNA secondary structure prediction.Frontiers in bioinformatics · 2024Article
- PrismNet: predicting protein-RNA interaction using in vivo RNA structural information.Nucleic acids research · 2023Article
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
- bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures.RNA (New York, N.Y.) · 2023Article
- Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA molecules fold into complex structures that are important across many biological processes. Recent technological developments have enabled transcriptome-wide probing of RNA secondary structure using nucleases and chemical modifiers. These approaches have been widely applied to capture RNA secondary structure in many studies, but gathering and presenting such data from very different technologies in a comprehensive and accessible way has been challenging. Existing RNA structure probing databases usually focus on low-throughput or very specific datasets. Here, we present a comprehensive RNA structure probing database called RASP (RNA Atlas of Structure Probing) by collecting 161 deduplicated transcriptome-wide RNA secondary structure probing datasets from 38 papers. RASP covers 18 species across animals, plants, bacteria, fungi, and also viruses, and categorizes 18 experimental methods including DMS-seq, SHAPE-Seq, SHAPE-MaP, and icSHAPE, etc. Specially, RASP curates the up-to-date datasets of several RNA secondary structure probing studies for the RNA genome of SARS-CoV-2, the RNA virus that caused the on-going COVID-19 pandemic. RASP also provides a user-friendly interface to query, browse, and visualize RNA structure profiles, offering a shortcut to accessing RNA secondary structures grounded in experimental data. The database is freely available at http://rasp.zhanglab.net.
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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.