Research Article
Persistent Homology on RNA Secondary Structure Space
@INPROCEEDINGS{10.4108/eai.3-12-2015.2262543, author={Adane Mamuye and Matteo Rucco}, title={Persistent Homology on RNA Secondary Structure Space}, proceedings={9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)}, publisher={ACM}, proceedings_a={BICT}, year={2016}, month={5}, keywords={persistent homology rna secondary structure topological invariant}, doi={10.4108/eai.3-12-2015.2262543} }- Adane Mamuye
Matteo Rucco
Year: 2016
Persistent Homology on RNA Secondary Structure Space
BICT
EAI
DOI: 10.4108/eai.3-12-2015.2262543
Abstract
In this ongoing work, we employ persistent homology to analyze the RNA suboptimal structure space and secondary structure space of 5s rRNA. Our basic idea is to measure the topological similarity of the suboptimal structures by sliding the minimum free energy window. The preliminary result shows that the more the energy window slides from the lowest minimum energy structure the more dissimilar the structures with the lowest one. In addition, persistent homology is also used to classify 5s rRNA of Archaea species into different family of classes. Our preliminary result shows that structural dissimilarity can be observed even for species that are grouped under the same genus.
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