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SETTER: web server for RNA structure comparison

The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is ac...

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Detalles Bibliográficos
Autores principales: Čech, Petr, Svozil, Daniel, Hoksza, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394248/
https://www.ncbi.nlm.nih.gov/pubmed/22693209
http://dx.doi.org/10.1093/nar/gks560
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author Čech, Petr
Svozil, Daniel
Hoksza, David
author_facet Čech, Petr
Svozil, Daniel
Hoksza, David
author_sort Čech, Petr
collection PubMed
description The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n(2)) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter.
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spelling pubmed-33942482012-07-30 SETTER: web server for RNA structure comparison Čech, Petr Svozil, Daniel Hoksza, David Nucleic Acids Res Articles The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n(2)) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter. Oxford University Press 2012-07 2012-06-11 /pmc/articles/PMC3394248/ /pubmed/22693209 http://dx.doi.org/10.1093/nar/gks560 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Čech, Petr
Svozil, Daniel
Hoksza, David
SETTER: web server for RNA structure comparison
title SETTER: web server for RNA structure comparison
title_full SETTER: web server for RNA structure comparison
title_fullStr SETTER: web server for RNA structure comparison
title_full_unstemmed SETTER: web server for RNA structure comparison
title_short SETTER: web server for RNA structure comparison
title_sort setter: web server for rna structure comparison
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394248/
https://www.ncbi.nlm.nih.gov/pubmed/22693209
http://dx.doi.org/10.1093/nar/gks560
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