Abstract
The RNA structure, the main predictor of biological function, is the result of the folding process. While the nucleotides in the RNA sequence rapidly coupled forming weak bonds, the spatial arrangement is a slow process. Although many computational approaches have been proposed to study the folding process of RNA, most of them do not consider the hierarchical aspect existing among the bonds. In this work, we propose to collapse nucleotides and bonds underpinning the primary and secondary structure of RNA in a unique label core congruent with the spatial configuration. A label core is represented as a term of generalized context-free grammar properly defined to support RNA structural reduction and analysis.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Andersen, J.E., Huang, F.W., Penner, R., Reidys, C.: Topology of RNA-RNA interaction structures. J. Comput. Biol. 7(19), 928–943 (2012)
Andronescu, M., Bereg, V., Hoos, H.H., Condon, A.: RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinform. 9(1), 340 (2008)
Giegerich, R., Steffen, P.: Implementing algebraic dynamic programming in the functional and the imperative programming paradigm. In: Boiten, E.A., Möller, B. (eds.) MPC 2002. LNCS, vol. 2386, pp. 1–20. Springer, Heidelberg (2002). https://doi.org/10.1007/3-540-45442-X_1
Grigoriev, A.: Analyzing genomes with cumulative skew diagrams. Nucl. Acids Res. 26(10), 2286–2290 (1998)
Harrison, M.A.: Introduction to Formal Language Theory. Addison-Wesley Longman Publishing Co., Inc., Boston (1978)
Holbrook, S.R., Kim, S.H.: RNA crystallography. Biopolym.: Orig. Res. Biomol. 44(1), 3–21 (1997)
Kasami, T., Seki, H., Fujii, M.: Generalized context-free grammars and multiple context-free grammars. Sys. Comput. Jpn. 20(7), 43–52 (1989)
Kjems, J., Egebjerg, J.: Modern methods for probing RNA structure. Curr. Opin. Biotechnol. 9(1), 59–65 (1998)
Maestri, S., Merelli, E.: Process calculi may reveal the equivalence lying at the heart of RNA and proteins. Sci. Rep. 9(559), 1–9 (2019)
Quadrini, M., Tesei, L., Merelli, E.: An algebraic language for RNA pseudoknots comparison. BMC Bioinform. 20(4), 161 (2019)
Quadrini, M., Merelli, E.: Loop-loop interaction metrics on RNA secondary structures with pseudoknots. In: Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS, pp. 29–37 (2018)
Quadrini, M., Merelli, E., Piergallini, R.: Loop grammars to identify RNA structural patterns. In: Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS, pp. 302–309. SciTePress (2019)
Reidys, C.: Combinatorial Computational Biology of RNA. Springer, New York (2011)
Yousef, M., Khalifa, W., Acar, I.E., Allmer, J.: MicroRNA categorization using sequence motifs and k-mers. BMC Bioinform. 18(1), e170 (2017)
Acknowledgements
We acknowledge the financial support of the Future and Emerging Technologies (FET) programme within the Seventh Framework Programme (FP7) for Research of the European Commission, under the FET-Proactive grant agreement TOPDRIM (www.topdrim.eu), number FP7-ICT- 318121.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Appendix A
Appendix A
In this appendix we list the molecules of the two group that we have downloaded from the RNA STRAND database.
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this paper
Cite this paper
Quadrini, M., Merelli, E., Piergallini, R. (2020). Label Core for Understanding RNA Structure. In: Cazzaniga, P., Besozzi, D., Merelli, I., Manzoni, L. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2019. Lecture Notes in Computer Science(), vol 12313. Springer, Cham. https://doi.org/10.1007/978-3-030-63061-4_16
Download citation
DOI: https://doi.org/10.1007/978-3-030-63061-4_16
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-63060-7
Online ISBN: 978-3-030-63061-4
eBook Packages: Computer ScienceComputer Science (R0)