ORCID Profile
0000-0002-2921-1157
Current Organisations
Research Centre of Medical Genetics
,
La Trobe University
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Publisher: BMJ
Date: 10-2023
Publisher: Wiley
Date: 03-2023
DOI: 10.1111/JPC.16357
Publisher: Springer International Publishing
Date: 2020
Publisher: Springer Science and Business Media LLC
Date: 12-2014
Publisher: World Scientific Pub Co Pte Lt
Date: 02-2018
DOI: 10.1142/S0219720018400012
Abstract: The discovery of thousands of long noncoding RNAs (lncRNAs) in mammals raises a question about their functionality. It has been shown that some of them are involved in post-transcriptional regulation of other RNAs and form inter-molecular duplexes with their targets. Sequence alignment tools have been used for transcriptome-wide prediction of RNA–RNA interactions. However, such approaches have poor prediction accuracy since they ignore RNA’s secondary structure. Application of the thermodynamics-based algorithms to long transcripts is not computationally feasible on a large scale. Here, we describe a new computational pipeline ASSA that combines sequence alignment and thermodynamics-based tools for efficient prediction of RNA–RNA interactions between long transcripts. To measure the hybridization strength, the sum energy of all the putative duplexes is computed. The main novelty implemented in ASSA is the ability to quickly estimate the statistical significance of the observed interaction energies. Most of the functional hybridizations between long RNAs were classified as statistically significant. ASSA outperformed 11 other tools in terms of the Area Under the Curve on two out of four test sets. Additionally, our results emphasized a unique property of the [Formula: see text] repeats with respect to the RNA–RNA interactions in the human transcriptome. ASSA is available at rojects/assa/
Publisher: Public Library of Science (PLoS)
Date: 29-10-2020
Publisher: Elsevier BV
Date: 05-2022
Location: Russian Federation
Location: United States of America
Location: United States of America
Location: United States of America
No related grants have been discovered for Desireé LaGrappe.