ArticleRNA (New York, N.Y.)2008
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Making Ends Meet or Just Meeting at the Ends? Assessing End-to-End Distance in Folded RNA Sequences and Other Branched Structures.Bulletin of mathematical biology · 2026Article
- R3DCID: circular interaction diagrams for RNA and DNA 3D structures of all sizes.RNA (New York, N.Y.) · 2026Article
- Graph-based RNA structural representation reveals determinants of subcellular localization.Briefings in bioinformatics · 2026Article
- Coevolution of RNase P and the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Hierarchical analysis of RNA secondary structures with pseudoknots based on sections.PLoS computational biology · 2026Article
- PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures.PLoS computational biology · 2025Article
- A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification.PloS one · 2025Article
- FURNA: A database for functional annotations of RNA structures.PLoS biology · 2024Article
- Knotify_V2.0: Deciphering RNA Secondary Structures with H-Type Pseudoknots and Hairpin Loops.Genes · 2024Article
- Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.Bioinformatics (Oxford, England) · 2024Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.Bioinformatics (Oxford, England) · 2023Article
- Biotite: new tools for a versatile Python bioinformatics library.BMC bioinformatics · 2023Article
- Article
- Metrics for RNA Secondary Structure Comparison.Methods in molecular biology (Clifton, N.J.) · 2023Article
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- The energy-spectrum of bicompatible sequences.Algorithms for molecular biology : AMB · 2021Article
- Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.PLoS computational biology · 2021Article
- IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles.Nucleic acids research · 2020Article
- LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pseudoknots are abundant in RNA structures. Many computational analyses require pseudoknot-free structures, which means that some of the base pairs in the knotted structure must be disregarded to obtain a nested structure. There is a surprising diversity of methods to perform this pseudoknot removal task, but these methods are often poorly described and studies can therefore be difficult to reproduce (in part, because different procedures may be intuitively obvious to different investigators). Here we provide a variety of algorithms for pseudoknot removal, some of which can incorporate sequence or alignment information in the removal process. We demonstrate that different methods lead to different results, which might affect structure-based analyses. This work thus provides a starting point for discussion of the extent to which these different methods recapture the underlying biological reality. We provide access to reference implementations through a web interface (at http://www.ibi.vu.nl/programs/k2nwww), and the source code is available in the PyCogent project.
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