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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-02-01
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| Series: | Biomolecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-273X/13/2/308 |
| _version_ | 1797622109487235072 |
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| author | Evangelos Makris Angelos Kolaitis Christos Andrikos Vrettos Moulos Panayiotis Tsanakas Christos Pavlatos |
| author_facet | Evangelos Makris Angelos Kolaitis Christos Andrikos Vrettos Moulos Panayiotis Tsanakas Christos Pavlatos |
| author_sort | Evangelos Makris |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-11T09:05:38Z |
| format | Article |
| id | doaj.art-0e69ef3d61b84719be7c6ebab5811175 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-11T09:05:38Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-0e69ef3d61b84719be7c6ebab58111752023-11-16T19:23:20ZengMDPI AGBiomolecules2218-273X2023-02-0113230810.3390/biom13020308Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal LoopsEvangelos Makris0Angelos Kolaitis1Christos Andrikos2Vrettos Moulos3Panayiotis Tsanakas4Christos Pavlatos5School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou St., 15780 Athens, GreeceSchool of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou St., 15780 Athens, GreeceSchool of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou St., 15780 Athens, GreeceSchool of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou St., 15780 Athens, GreeceSchool of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou St., 15780 Athens, GreeceHellenic Air Force Academy, Dekelia Air Base, Acharnes, 13671 Athens, GreeceThe 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.https://www.mdpi.com/2218-273X/13/2/308H-type pseudoknot structureRNAbulgesinternal loopsparserCFG |
| spellingShingle | Evangelos Makris Angelos Kolaitis Christos Andrikos Vrettos Moulos Panayiotis Tsanakas Christos Pavlatos Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops Biomolecules H-type pseudoknot structure RNA bulges internal loops parser CFG |
| 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 | H-type pseudoknot structure RNA bulges internal loops parser CFG |
| url | https://www.mdpi.com/2218-273X/13/2/308 |
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