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SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments

RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in...

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Autores principales: Piątkowski, Paweł, Jabłońska, Jagoda, Żyła, Adriana, Niedziałek, Dorota, Matelska, Dorota, Jankowska, Elżbieta, Waleń, Tomasz, Dawson, Wayne K., Bujnicki, Janusz M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766185/
https://www.ncbi.nlm.nih.gov/pubmed/28934487
http://dx.doi.org/10.1093/nar/gkx631
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author Piątkowski, Paweł
Jabłońska, Jagoda
Żyła, Adriana
Niedziałek, Dorota
Matelska, Dorota
Jankowska, Elżbieta
Waleń, Tomasz
Dawson, Wayne K.
Bujnicki, Janusz M.
author_facet Piątkowski, Paweł
Jabłońska, Jagoda
Żyła, Adriana
Niedziałek, Dorota
Matelska, Dorota
Jankowska, Elżbieta
Waleń, Tomasz
Dawson, Wayne K.
Bujnicki, Janusz M.
author_sort Piątkowski, Paweł
collection PubMed
description RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in the characterization of functional motifs and in structure prediction by comparative modeling. However, compared to the numerous methods for protein structure superposition, there are few tools dedicated to the superimposing of RNA 3D structures. Here, we present SupeRNAlign (v1.3.1), a new method for flexible superposition of RNA 3D structures, and SupeRNAlign-Coffee—a workflow that combines SupeRNAlign with T-Coffee for inferring structure-based sequence alignments. The methods have been benchmarked with eight other methods for RNA structural superposition and alignment. The benchmark included 151 structures from 32 RNA families (with a total of 1734 pairwise superpositions). The accuracy of superpositions was assessed by comparing structure-based sequence alignments to the reference alignments from the Rfam database. SupeRNAlign and SupeRNAlign-Coffee achieved significantly higher scores than most of the benchmarked methods: SupeRNAlign generated the most accurate sequence alignments among the structure superposition methods, and SupeRNAlign-Coffee performed best among the sequence alignment methods.
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spelling pubmed-57661852018-01-19 SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments Piątkowski, Paweł Jabłońska, Jagoda Żyła, Adriana Niedziałek, Dorota Matelska, Dorota Jankowska, Elżbieta Waleń, Tomasz Dawson, Wayne K. Bujnicki, Janusz M. Nucleic Acids Res Methods Online RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in the characterization of functional motifs and in structure prediction by comparative modeling. However, compared to the numerous methods for protein structure superposition, there are few tools dedicated to the superimposing of RNA 3D structures. Here, we present SupeRNAlign (v1.3.1), a new method for flexible superposition of RNA 3D structures, and SupeRNAlign-Coffee—a workflow that combines SupeRNAlign with T-Coffee for inferring structure-based sequence alignments. The methods have been benchmarked with eight other methods for RNA structural superposition and alignment. The benchmark included 151 structures from 32 RNA families (with a total of 1734 pairwise superpositions). The accuracy of superpositions was assessed by comparing structure-based sequence alignments to the reference alignments from the Rfam database. SupeRNAlign and SupeRNAlign-Coffee achieved significantly higher scores than most of the benchmarked methods: SupeRNAlign generated the most accurate sequence alignments among the structure superposition methods, and SupeRNAlign-Coffee performed best among the sequence alignment methods. Oxford University Press 2017-09-19 2017-07-20 /pmc/articles/PMC5766185/ /pubmed/28934487 http://dx.doi.org/10.1093/nar/gkx631 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution 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 Methods Online
Piątkowski, Paweł
Jabłońska, Jagoda
Żyła, Adriana
Niedziałek, Dorota
Matelska, Dorota
Jankowska, Elżbieta
Waleń, Tomasz
Dawson, Wayne K.
Bujnicki, Janusz M.
SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments
title SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments
title_full SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments
title_fullStr SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments
title_full_unstemmed SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments
title_short SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments
title_sort supernalign: a new tool for flexible superposition of homologous rna structures and inference of accurate structure-based sequence alignments
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766185/
https://www.ncbi.nlm.nih.gov/pubmed/28934487
http://dx.doi.org/10.1093/nar/gkx631
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