SETTER: web server for RNA structure comparison

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.

Reverse Watson-Crick purine-purine base pairs — the Sharp-turn motif and other structural consequences in functional RNAs

“…Structural alignment is necessary for this purpose, since, homologous RNAs from different organisms have slightly different sequence and structure and consequently have different residue numbering. We have used SETTER [32][33][34][35] algorithm for structural alignment of RNAs. For the purpose of 3D structural alignment, SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) divides an RNA structure into a set of nonoverlapping structural elements called generalized secondary structure units (GSSUs).…”

The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs

“…Other workers have developed similar methods to identify, extract, and cluster RNA 3D motifs and websites to make them available in searchable formats [2–6]. This contribution is not meant as a comprehensive comparison of all the available methods, but as an attempt to provide detailed explanation of our own approach, as well as an extensive discussion of its limitations and the opportunities for future work in the field.…”

Fast alignment and comparison of RNA structures

“…This is a major difference compared with RNA secondary-structure aligners (locaRNA, RNAforrester), which cannot take advantage of other common structural motifs. Most importantly, the labels are not discrete as in a typical Results for SETTER are from Cech et al (2012). Results for R3D Align, ARTS, SARA and DIAL are taken from Rahrig et al (2010).…”

“…SARA (Capriotti and Marti-Renom, 2008) follows an approach inspired by the MAMMOTH programme for protein structure alignment (Ortiz et al, 2002). The most recent approach, SETTER, divides RNA structures into non-overlapping secondary structure elements (Cech et al, 2012). All of these methods are sensitive to the geometry of specific sites rather than larger pieces of structure.…”

“…Both SETTER and R3D Align (Cech et al, 2012;Rahrig et al, 2010) were compared on the basis of the alignment of two 16S rRNA structures against ARTS, SARA and DIAL. Table 2 shows little difference between the results from FRIEs and the other approaches.…”