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Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops

The accurate “base pairing” in RNA molecules, which leads to the prediction of RNA secondary structures, is crucial in order to explain unknown biological operations. Recently, COVID-19, a widespread disease, has caused many deaths, affecting humanity in an unprecedented way. SARS-CoV-2, a single-st...

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Detalles Bibliográficos
Autores principales: Makris, Evangelos, Kolaitis, Angelos, Andrikos, Christos, Moulos, Vrettos, Tsanakas, Panayiotis, Pavlatos, Christos
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9953189/
https://www.ncbi.nlm.nih.gov/pubmed/36830677
http://dx.doi.org/10.3390/biom13020308
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author Makris, Evangelos
Kolaitis, Angelos
Andrikos, Christos
Moulos, Vrettos
Tsanakas, Panayiotis
Pavlatos, Christos
author_facet Makris, Evangelos
Kolaitis, Angelos
Andrikos, Christos
Moulos, Vrettos
Tsanakas, Panayiotis
Pavlatos, Christos
author_sort Makris, Evangelos
collection PubMed
description The accurate “base pairing” in RNA molecules, which leads to the prediction of RNA secondary structures, is crucial in order to explain unknown biological operations. Recently, COVID-19, a widespread disease, has caused many deaths, affecting humanity in an unprecedented way. SARS-CoV-2, a single-stranded RNA virus, has shown the significance of analyzing these molecules and their structures. This paper aims to create a pioneering framework in the direction of predicting specific RNA structures, leveraging syntactic pattern recognition. The proposed framework, Knotify+, addresses the problem of predicting H-type pseudoknots, including bulges and internal loops, by featuring the power of context-free grammar (CFG). We combine the grammar’s advantages with maximum base pairing and minimum free energy to tackle this ambiguous task in a performant way. Specifically, our proposed methodology, Knotify+, outperforms state-of-the-art frameworks with regards to its accuracy in core stems prediction. Additionally, it performs more accurately in small sequences and presents a comparable accuracy rate in larger ones, while it requires a smaller execution time compared to well-known platforms. The Knotify+ source code and implementation details are available as a public repository on GitHub.
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spelling pubmed-99531892023-02-25 Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops Makris, Evangelos Kolaitis, Angelos Andrikos, Christos Moulos, Vrettos Tsanakas, Panayiotis Pavlatos, Christos Biomolecules Article The accurate “base pairing” in RNA molecules, which leads to the prediction of RNA secondary structures, is crucial in order to explain unknown biological operations. Recently, COVID-19, a widespread disease, has caused many deaths, affecting humanity in an unprecedented way. SARS-CoV-2, a single-stranded RNA virus, has shown the significance of analyzing these molecules and their structures. This paper aims to create a pioneering framework in the direction of predicting specific RNA structures, leveraging syntactic pattern recognition. The proposed framework, Knotify+, addresses the problem of predicting H-type pseudoknots, including bulges and internal loops, by featuring the power of context-free grammar (CFG). We combine the grammar’s advantages with maximum base pairing and minimum free energy to tackle this ambiguous task in a performant way. Specifically, our proposed methodology, Knotify+, outperforms state-of-the-art frameworks with regards to its accuracy in core stems prediction. Additionally, it performs more accurately in small sequences and presents a comparable accuracy rate in larger ones, while it requires a smaller execution time compared to well-known platforms. The Knotify+ source code and implementation details are available as a public repository on GitHub. MDPI 2023-02-06 /pmc/articles/PMC9953189/ /pubmed/36830677 http://dx.doi.org/10.3390/biom13020308 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Makris, Evangelos
Kolaitis, Angelos
Andrikos, Christos
Moulos, Vrettos
Tsanakas, Panayiotis
Pavlatos, Christos
Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops
title Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops
title_full Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops
title_fullStr Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops
title_full_unstemmed Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops
title_short Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops
title_sort knotify+: toward the prediction of rna h-type pseudoknots, including bulges and internal loops
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9953189/
https://www.ncbi.nlm.nih.gov/pubmed/36830677
http://dx.doi.org/10.3390/biom13020308
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