ArticleIAENG international journal of computer science2017
Partitioning and Classification of RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions Using a Graph-Theoretical Approach.
Article in IAENG international journal of computer science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed.
- Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.International journal of molecular sciences · 2022Article
- To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element.Journal of the American Chemical Society · 2021Article
- To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element.bioRxiv : the preprint server for biology · 2021Article
- An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.Methods (San Diego, Calif.) · 2019Article
- Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.Genes · 2018Article
- Adventures with RNA graphs.Methods (San Diego, Calif.) · 2018Review
- Partitioning and Classification of RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions Using a Graph-Theoretical Approach.IAENG international journal of computer science · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In this paper we present a linear-time algorithm to partition dual graphs into maximal topological components called blocks and determine whether each block contains a pseudoknot or not. We show that a block contains a pseudoknot if and only if the block has a vertex of degree 3 or more; this characterization allows us to efficiently isolate smaller RNA fragments and classify them as pseudoknotted or pseudoknot-free regions, while keeping these sub-structures intact. Applications to RNA design can be envisioned since modular building blocks with intact pseudoknots can be combined to form new constructs.
Indexed as
Identifiers
30474081PMC6250053What OpenQuestion holds
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.