ArticleBMC bioinformatics2011
RAG: an update to the RNA-As-Graphs resource.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Graph-CRISPR: a gene editing efficiency prediction model based on graph neural network with integrated sequence and secondary structure feature extraction.Briefings in bioinformatics · 2025Article
- RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.International journal of molecular sciences · 2022Article
- Fuzzy RNA recognition by the Trypanosoma brucei editosome.Nucleic acids research · 2022Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- Diagrammatic approaches to RNA structures with trinucleotide repeats.Biophysical journal · 2021Article
- Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments.NAR genomics and bioinformatics · 2021Article
- Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction.Nucleic acids research · 2020Article
- Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library.Biochimica et biophysica acta. General subjects · 2020Article
- Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies.Journal of structural biology · 2020Article
- VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures.Journal of structural biology · 2019Article
- An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.Methods (San Diego, Calif.) · 2019Article
- A pipeline for computational design of novel RNA-like topologies.Nucleic acids research · 2018Article
- Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.Genes · 2018Article
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
- bpRNA: large-scale automated annotation and analysis of RNA secondary structure.Nucleic acids research · 2018Article
- Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.The journal of physical chemistry. B · 2018Article
- F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.Journal of molecular biology · 2017Article
- Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.Nucleic acids research · 2017Article
- Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundIn 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structure motifs using clustering and build-up approaches. With the increased availability of secondary structures in recent years, we update the RAG resource and provide various improvements for analyzing RNA structures. DESCRIPTION: Our RAG update includes a new supervised clustering algorithm that can suggest RNA motifs that may be "RNA-like". We use this utility to describe RNA motifs as three classes: existing, RNA-like, and non-RNA-like. This produces 126 tree and 16,658 dual graphs as candidate RNA-like topologies using the supervised clustering algorithm with existing RNAs serving as the training data. A comparison of this clustering approach to an earlier method shows considerable improvements. Additional RAG features include greatly expanded search capabilities, an interface to better utilize the benefits of relational database, and improvements to several of the utilities such as directed/labeled graphs and a subgraph search program.
conclusionsThe RAG updates presented here augment the database's intended function - stimulating the search for novel RNA functionality - by classifying available motifs, suggesting new motifs for design, and allowing for more specific searches for specific topologies. The updated RAG web resource offers users a graph-based tool for exploring available RNA motifs and suggesting new RNAs for design.
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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.