ArticleNucleic acids research2012
Global or local? Predicting secondary structure and accessibility in mRNAs.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed.
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
- Accurately modeling RNase H-mediated antisense oligonucleotide efficacy.Molecular therapy. Nucleic acids · 2026Article
- RNA binding motif protein RBM41 promotes colorectal tumorigenesis by impeding the maturation of NDRG1 pre-mRNA.Cell death discovery · 2026Article
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- 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
- Exploring the Boundaries of Modern Quantum Annealers with RNA Structure Prediction.The journal of physical chemistry. B · 2026Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for biology · 2025Article
- Neuropilin-1: A Conserved Entry Receptor for SARS-CoV-2 and a Potential Therapeutic Target.Biomedicines · 2025Article
- VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction.NAR genomics and bioinformatics · 2025Article
- Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.Research square · 2024Article
- Smaug regulates germ plasm assembly and primordial germ cell number in Drosophila embryos.Science advances · 2024Article
- Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes.Biology · 2023Article
- RNA Secondary Structure Alteration Caused by Single Nucleotide Variants.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Linear-Time Algorithms for RNA Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- DeepRaccess: high-speed RNA accessibility prediction using deep learning.Frontiers in bioinformatics · 2023Article
- Genome-Wide RNA Secondary Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Evolutionary Conservation of RNA Secondary Structure.Methods in molecular biology (Clifton, N.J.) · 2023Article
- mintRULS: Prediction of miRNA-mRNA Target Site Interactions Using Regularized Least Square Method.Genes · 2022Article
- RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.PLoS computational biology · 2022Article
44 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Determining the structural properties of mRNA is key to understanding vital post-transcriptional processes. As experimental data on mRNA structure are scarce, accurate structure prediction is required to characterize RNA regulatory mechanisms. Although various structure prediction approaches are available, it is often unclear which to choose and how to set their parameters. Furthermore, no standard measure to compare predictions of local structure exists. We assessed the performance of different methods using two types of data: transcriptome-wide enzymatic probing information and a large, curated set of cis-regulatory elements. To compare the approaches, we introduced structure accuracy, a measure that is applicable to both global and local methods. Our results showed that local folding was more accurate than the classic global approach. We investigated how the locality parameters, maximum base pair span and window size, influenced the prediction performance. A span of 150 provided a reasonable balance between maximizing the number of accurately predicted base pairs, while minimizing effects of incorrect long-range predictions. We characterized the error at artificial sequence ends, which we reduced by setting the window size sufficiently greater than the maximum span. Our method, LocalFold, diminished all border effects and produced the most robust performance.
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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.