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Oxford University Press, Nucleic Acids Research, W1(40), p. W42-W48, 2012

DOI: 10.1093/nar/gks560

BioMed Central, BMC Bioinformatics, 1(16)

DOI: 10.1186/s12859-015-0696-8

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SETTER: web server for RNA structure comparison

Journal article published in 2012 by Petr Čech, Daniel Svozil ORCID, David Hoksza
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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(n2) 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.