ArticleBioinformatics (Oxford, England)2023
Modified RNAs and predictions with the ViennaRNA Package.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 21 citations in OpenAlex.
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- Long Noncoding RNA Isoform Specificity and Chemical Modification on tRNA-Derived Fragments Leading to Divergent Functions.The American journal of pathology · 2026Review
- RNA Aptamers and Epitranscriptomics: Charting Unexplored Territories in RNA Biology.Molecular diagnosis & therapy · 2026Review
- De Novo Variation in Autism by Sex and Diagnostic Status in 41,367 Parent-Child Trios.medRxiv : the preprint server for health sciences · 2026Article
- Leveraging Foundation Models for the Characterization of Small-RNA Properties.Computational and structural biotechnology journal · 2026Article
- A method for estimating energy parameters of RNAs by differentiating base-pairing probabilities.NAR genomics and bioinformatics · 2025Article
- Genome-Wide Identification of MicroRNAs and Immune-Related Proteins Provides Insights into Antiviral Adaptations in Common Vampire Bat.Animals : an open access journal from MDPI · 2025Article
- Human Synthetic Biology and Programmable Gene Regulation Control.Annual review of genomics and human genetics · 2025Review
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Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
motivationIn living organisms, many RNA molecules are modified post-transcriptionally. This turns the widely known four-letter RNA alphabet ACGU into a much larger one with currently more than 300 known distinct modified bases. The roles for the majority of modified bases remain uncertain, but many are already well-known for their ability to influence the preferred structures that an RNA may adopt. In fact, tRNAs sometimes require certain modifications to fold into their cloverleaf shaped structure. However, predicting the structure of RNAs with base modifications is still difficult due to the lack of efficient algorithms that can deal with the extended sequence alphabet, as well as missing parameter sets that account for the changes in stability induced by the modified bases.
resultsWe present an approach to include sparse energy parameter data for modified bases into the ViennaRNA Package. Our method does not require any changes to the underlying efficient algorithms but instead uses a set of plug-in constraints that adapt the predictions in terms of loop evaluation at runtime. These adaptations are efficient in the sense that they are only performed for loops where additional parameters are actually available for. In addition, our approach also facilitates the inclusion of more modified bases as soon as further parameters become available. AVAILABILITY AND IMPLEMENTATION: Source code and documentation are available at https://www.tbi.univie.ac.at/RNA.
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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.