ArticleBioinformatics (Oxford, England)2015
StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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
26 citing papers in PubMed.
- In vivo structure probing of RNA inRNA (New York, N.Y.) · 2023Article
- Transcriptome-wide probing reveals RNA thermometers that regulate translation of glycerol permease genes inRNA (New York, N.Y.) · 2023Article
- Using DMS-MaPseq to uncover the roles of DEAD-box proteins in ribosome assembly.Methods (San Diego, Calif.) · 2022Article
- Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome.International journal of molecular sciences · 2021Article
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- RNAProbe: a web server for normalization and analysis of RNA structure probing data.Nucleic acids research · 2020Article
- Tissue-specific changes in the RNA structurome mediate salinity response inRNA (New York, N.Y.) · 2020Article
- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.GigaScience · 2019Article
- An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!Methods in molecular biology (Clifton, N.J.) · 2019Article
- Technique Development for Probing RNA Structure In Vivo and Genome-Wide.Cold Spring Harbor perspectives in biology · 2018Review
- Article
- Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements.Nucleic acids research · 2018Article
- Mapping platinum adducts on yeast ribosomal RNA using high-throughput sequencing.Chemical communications (Cambridge, England) · 2017Article
- High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast.Nature communications · 2017Article
- Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo.Nucleic acids research · 2017Article
- Multiplex Aptamer Discovery through Apta-Seq and Its Application to ATP Aptamers Derived from Human-Genomic SELEX.ACS chemical biology · 2017Article
- PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays.Cell systems · 2017Article
- Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.Quantitative biology (Beijing, China) · 2017Article
- SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data.Bioinformatics (Oxford, England) · 2017Article
- FoldAtlas: a repository for genome-wide RNA structure probing data.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationRNAs fold into complex structures that are integral to the diverse mechanisms underlying RNA regulation of gene expression. Recent development of transcriptome-wide RNA structure profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise.
resultsWe present a new platform, StructureFold, that provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user-friendly web interface or via local installation. The variation in transcript abundance and length that prevails in living cells and consequently causes variation in the counts of structure-probing events between transcripts is accounted for. Accordingly, StructureFold is applicable to RNA structural profiling data obtained in vivo as well as to in vitro or in silico datasets. StructureFold is deployed via the Galaxy platform. AVAILABILITY AND IMPLEMENTATION: StructureFold is freely available as a component of Galaxy available at: https://usegalaxy.org/. CONTACT: yxt148@psu.edu or sma3@psu.edu SUPPLEMENTARY 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.