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SETTER: web server for RNA structure comparison.

Čech P. 1; Hoksza D.1,2; Svozil D.1

1Laboratory of Informatics and Chemistry, Institute of Chemical Technology Prague, 16628 Czech Republic

2SIRET Research Group, Department of Software Engineering, FMP, Charles University in Prague, 11800 Czech Republic

Nucleic Acids Research W1: W42-W48 2012

The transfer of genetic information was, for a long time, considered as the main biological function of RNA. However, recent evidence shows that all organisms contain a wealth of small untranslated RNAs (so-called non-protein coding RNAs – ncRNAs) that function in a variety of cellular processes. These findings have directly challenged our understanding of biological regulation and extended our view of RNA as an important player in the development of complex organisms. The function of RNA is largely determined by its 3D structure. Thus, the development of methods for the comparative RNA function annotation based on structural similarity became the important part of contemporary bioinformatics research. Though several such methods are available, they restrict the size of aligned structures, as well as achieve low speeds when aligning large RNA molecules. Therefore, we have developed the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER algorithm is, at the moment, the fastest approach for the structural alignment of RNA molecules. Not only it offers unprecedented speed even for largest RNA structures (no size limit is imposed), but also its accuracy is comparable to other, though slower, approaches. To simplify the access to our method, we have also developed a freely accessible web server that serves as an intuitive interface to the RNA structure alignment by SETTER. We believe that this offering will bolster the use of RNA structural and functional annotation between a broad scientific community.
D. Svozil instigated the project, participated in the development of the algorithm, software and the web server, collected data sets and benchmarked the algorithm. D. Hoksza proposed and developed the algorithm and software. P. Čech developed and implemented the SETTER web server. Most of the project was made on Institute of Chemical Technology, only the software was partially developer on the co-operating institution.

Updated: 16.1.2015 10:55, Author: Lenka Matějová

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