FRASS: the web-server for RNA structural comparison

Svetlana Kirillova,Oliviero Carugo,Silvio Ce Tosatto

doi:10.1186/1471-2105-11-327

Svetlana Kirillova, Oliviero Carugo + Show 1 more

Open Access

https://doi.org/10.1186/1471-2105-11-327

Copy DOI

Abstract

BackgroundThe impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.ResultsThe FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method.ConclusionsThe FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

Highlights

The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison
The flexibility of the RNA backbone, limited to six torsion angles per base, is restricted. It was shown [1,2,3] that RNA molecules can be represented by using collections of stable structures or structural motifs
PRIMOS [4] uses the 3D worm representation of a RNA molecule in which two coordinates correspond to the pseudo-torsions describing the nucleotide conformation and a third coordinate defines the sequence

Summary

Introduction

The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules. The flexibility of the RNA backbone, limited to six torsion angles per base, is restricted. It was shown [1,2,3] that RNA molecules can be represented by using collections of stable structures or structural motifs. Most of the 3D tools developed for RNA molecules handle only local structural elements or motifs. PRIMOS was used to perform structural motif searches and is limited to the comparison of different conformations of the same molecule. COMPADRES [5] is a modified ver-

Methods

Results

Conclusion