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New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation

MOTIVATION: Understanding the formation, architecture and roles of pseudoknots in RNA structures are one of the most difficult challenges in RNA computational biology and structural bioinformatics. Methods predicting pseudoknots typically perform this with poor accuracy, often despite experimental d...

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Autores principales: Antczak, Maciej, Popenda, Mariusz, Zok, Tomasz, Zurkowski, Michal, Adamiak, Ryszard W, Szachniuk, Marta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905660/
https://www.ncbi.nlm.nih.gov/pubmed/29236971
http://dx.doi.org/10.1093/bioinformatics/btx783
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author Antczak, Maciej
Popenda, Mariusz
Zok, Tomasz
Zurkowski, Michal
Adamiak, Ryszard W
Szachniuk, Marta
author_facet Antczak, Maciej
Popenda, Mariusz
Zok, Tomasz
Zurkowski, Michal
Adamiak, Ryszard W
Szachniuk, Marta
author_sort Antczak, Maciej
collection PubMed
description MOTIVATION: Understanding the formation, architecture and roles of pseudoknots in RNA structures are one of the most difficult challenges in RNA computational biology and structural bioinformatics. Methods predicting pseudoknots typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ in terms of pseudoknots’ recognition and revealing their nature. A few ways of pseudoknot classification exist, most common ones refer to a genus or order. Following the latter one, we propose new algorithms that identify pseudoknots in RNA structure provided in BPSEQ format, determine their order and encode in dot-bracket-letter notation. The proposed encoding aims to illustrate the hierarchy of RNA folding. RESULTS: New algorithms are based on dynamic programming and hybrid (combining exhaustive search and random walk) approaches. They evolved from elementary algorithm implemented within the workflow of RNA FRABASE 1.0, our database of RNA structure fragments. They use different scoring functions to rank dissimilar dot-bracket representations of RNA structure. Computational experiments show an advantage of new methods over the others, especially for large RNA structures. AVAILABILITY AND IMPLEMENTATION: Presented algorithms have been implemented as new functionality of RNApdbee webserver and are ready to use at http://rnapdbee.cs.put.poznan.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-59056602018-04-23 New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation Antczak, Maciej Popenda, Mariusz Zok, Tomasz Zurkowski, Michal Adamiak, Ryszard W Szachniuk, Marta Bioinformatics Original Papers MOTIVATION: Understanding the formation, architecture and roles of pseudoknots in RNA structures are one of the most difficult challenges in RNA computational biology and structural bioinformatics. Methods predicting pseudoknots typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ in terms of pseudoknots’ recognition and revealing their nature. A few ways of pseudoknot classification exist, most common ones refer to a genus or order. Following the latter one, we propose new algorithms that identify pseudoknots in RNA structure provided in BPSEQ format, determine their order and encode in dot-bracket-letter notation. The proposed encoding aims to illustrate the hierarchy of RNA folding. RESULTS: New algorithms are based on dynamic programming and hybrid (combining exhaustive search and random walk) approaches. They evolved from elementary algorithm implemented within the workflow of RNA FRABASE 1.0, our database of RNA structure fragments. They use different scoring functions to rank dissimilar dot-bracket representations of RNA structure. Computational experiments show an advantage of new methods over the others, especially for large RNA structures. AVAILABILITY AND IMPLEMENTATION: Presented algorithms have been implemented as new functionality of RNApdbee webserver and are ready to use at http://rnapdbee.cs.put.poznan.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2018-04-15 2017-12-11 /pmc/articles/PMC5905660/ /pubmed/29236971 http://dx.doi.org/10.1093/bioinformatics/btx783 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Original Papers
Antczak, Maciej
Popenda, Mariusz
Zok, Tomasz
Zurkowski, Michal
Adamiak, Ryszard W
Szachniuk, Marta
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
title New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
title_full New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
title_fullStr New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
title_full_unstemmed New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
title_short New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
title_sort new algorithms to represent complex pseudoknotted rna structures in dot-bracket notation
topic Original Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905660/
https://www.ncbi.nlm.nih.gov/pubmed/29236971
http://dx.doi.org/10.1093/bioinformatics/btx783
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