An algebraic representation for tree alignment of RNA pseudoknotted structures
- Published
- Accepted
- Subject Areas
- Bioinformatics
- Keywords
- RNA Algebraic Representation, pseudoknots comparison, tree alignment
- Copyright
- © 2017 Quadrini et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. An algebraic representation for tree alignment of RNA pseudoknotted structures. PeerJ Preprints 5:e3327v1 https://doi.org/10.7287/peerj.preprints.3327v1
Abstract
The methods proposed in the literature for RNA comparison focus mainly on pseudoknot free structures. The comparison of pseudoknotted structures is still a challenge. In this work, we propose a new algebraic representation of RNA secondary structures based on relations among hairpins in terms of nesting, crossing, and concatenation. Such algebraic representation is obtained from a defined multiple context-free grammar, which maps any kind of RNA secondary structures into extended trees, i.e., ordered trees where internal nodes are labeled with algebraic operators and leaves are labeled with loops. These extended trees permit the definition of the RNA secondary structure comparison as a tree alignment problem.
Author Comment
This is an abstract which has been accepted for the NETTAB 2017 Workshop