Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs
Abstract
:1. Introduction
2. Materials and Methods
2.1. RNA Dual Graph Representation
- An RNA stem (or helix) with at least two canonical base pairs is considered as a vertex.
- Each loop strand between two helices is denoted as an edge. Single-residue bulges and internal loops with only one nucleotide in each strand are ignored.
- Uninterrupted hairpin loops (including helical ends) are represented as self loops.
- Unpaired bases or helical ends at the 5 and 3 ends of RNA molecules are not represented.
2.2. Dual Graph Enumeration
2.3. Dual Graph Partitioning Algorithm
2.4. Representative Set of RNA Structures
2.5. Defining Existing Dual Graph Topologies
3. Results
3.1. Partitioning Dual Graphs into Subgraphs
3.2. Submotifs in Ribosomal RNAs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Jain, S.; Bayrak, C.S.; Petingi, L.; Schlick, T. Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs. Genes 2018, 9, 371. https://doi.org/10.3390/genes9080371
Jain S, Bayrak CS, Petingi L, Schlick T. Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs. Genes. 2018; 9(8):371. https://doi.org/10.3390/genes9080371
Chicago/Turabian StyleJain, Swati, Cigdem S. Bayrak, Louis Petingi, and Tamar Schlick. 2018. "Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs" Genes 9, no. 8: 371. https://doi.org/10.3390/genes9080371
APA StyleJain, S., Bayrak, C. S., Petingi, L., & Schlick, T. (2018). Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs. Genes, 9(8), 371. https://doi.org/10.3390/genes9080371