ArticleNucleic acids research2016
Rtools: a web server for various secondary structural analyses on single RNA sequences.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- The FIBRILLIN multigene family in tomato, their roles in plastoglobuli structure and metabolism.The Plant journal : for cell and molecular biology · 2025Article
- M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops.Cell death & disease · 2024Article
- Diagnostic and Therapeutic Aptamers: A Promising Pathway to Improved Cardiovascular Disease Management.JACC. Basic to translational science · 2024Review
- Exploring the landscape of tools and resources for the analysis of long non-coding RNAs.Computational and structural biotechnology journal · 2023Review
- Rtools: A Web Server for Various Secondary Structural Analyses on Single RNA Sequences.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Aptamers targeting amyloidogenic proteins and their emerging role in neurodegenerative diseases.The Journal of biological chemistry · 2022Review
- Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements.NAR genomics and bioinformatics · 2021Article
- Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding.RSC advances · 2019Article
- SilentMutations (SIM): A tool for analyzing long-range RNA-RNA interactions in viral genomes and structured RNAs.Virus research · 2019Article
- Advances in therapeutic bacterial antisense biotechnology.Applied microbiology and biotechnology · 2018Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD.
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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.