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Open Access Software

FRASS: the web-server for RNA structural comparison

Svetlana Kirillova1*, Silvio CE Tosatto2 and Oliviero Carugo13

Author Affiliations

1 Department of Structural and Computational Biology, Max F Perutz Laboratories, Vienna University, Campus Vienna Biocenter 5, A-1030 Vienna, Austria

2 Department of Biology, Universita' di Padova, Viale G Colombo 3, I-35121 Padova, Italy

3 Department of General Chemistry, Pavia University, Viele Taramelli 12, I-27100 Pavia, Italy

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BMC Bioinformatics 2010, 11:327  doi:10.1186/1471-2105-11-327

Published: 16 June 2010

Abstract

Background

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.

Results

The 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.

Conclusions

The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.