ArticleRNA (New York, N.Y.)2009
Computational identification of riboswitches based on RNA conserved functional sequences and conformations.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 60 citations in OpenAlex.
- RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation.Nucleic acids research · 2025Article
- Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning.PloS one · 2025Article
- Article
- A systematic search for RNA structural switches across the human transcriptome.Nature methods · 2024Article
- Expression of stress responsive genes enablesFrontiers in microbiology · 2024Article
- A novel riboswitch classification based on imbalanced sequences achieved by machine learning.PLoS computational biology · 2020Article
- Identification and characterisation of thiamine pyrophosphate (TPP) riboswitch in Elaeis guineensis.PloS one · 2020Article
- Riboflow: Using Deep Learning to Classify Riboswitches With ∼99% Accuracy.Frontiers in bioengineering and biotechnology · 2020Article
- Regulatory context drives conservation of glycine riboswitch aptamers.PLoS computational biology · 2019Article
- Small-Molecule-Binding Riboswitches.Microbiology spectrum · 2018Review
- Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi.Scientific reports · 2018Article
- An Archaeal Fluoride-Responsive Riboswitch Provides an Inducible Expression System for Hyperthermophiles.Applied and environmental microbiology · 2018Article
- Transcription and translation of the sigG gene is tuned for proper execution of the switch from early to late gene expression in the developing Bacillus subtilis spore.PLoS genetics · 2018Article
- Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.Frontiers in genetics · 2017Review
- Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria.PloS one · 2017Article
- RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.Nucleic acids research · 2015Article
- Molecular dissection of a Borrelia burgdorferi in vivo essential purine transport system.Infection and immunity · 2015Article
- A new approach for detecting riboswitches in DNA sequences.Bioinformatics (Oxford, England) · 2014Article
- Analysing RNA-kinetics based on folding space abstraction.BMC bioinformatics · 2014Article
- Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.International journal of bioinformatics research and applications · 2014Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are cis-acting genetic regulatory elements within a specific mRNA that can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, an increasing number of riboswitches have been identified in different species and investigated for their roles in regulatory functions. Both the sequence contexts and structural conformations are important characteristics of riboswitches. None of the previously developed tools, such as covariance models (CMs), Riboswitch finder, and RibEx, provide a web server for efficiently searching homologous instances of known riboswitches or considers two crucial characteristics of each riboswitch, such as the structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method for identifying 12 kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction, which makes it possible to have an accurate and convenient web server for biologists to obtain the results of their analysis of a given mRNA sequence. RiboSW is now available on the web at http://RiboSW.mbc.nctu.edu.tw/.
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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.