Nucleic Acids Research Advance Access published online on May 29, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp433
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Web Server Issue |
SARA: a server for function annotation of RNA structures
Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
*To whom correspondence should be addressed. Tel: +34 96 328 96 80; Fax: +34 96 328 97 01; Email: mmarti{at}cipf.es
Received February 8, 2009. Revised May 5, 2009. Accepted May 11, 2009.
Recent interest in non-coding RNA transcripts has resulted in a rapid increase of deposited RNA structures in the Protein Data Bank. However, a characterization and functional classification of the RNA structure and function space have only been partially addressed. Here, we introduce the SARA program for pair-wise alignment of RNA structures as a web server for structure-based RNA function assignment. The SARA server relies on the SARA program, which aligns two RNA structures based on a unit-vector root-mean-square approach. The likely accuracy of the SARA alignments is assessed by three different P-values estimating the statistical significance of the sequence, secondary structure and tertiary structure identity scores, respectively. Our benchmarks, which relied on a set of 419 RNA structures with known SCOR structural class, indicate that at a negative logarithm of mean P-value higher or equal than 2.5, SARA can assign the correct or a similar SCOR class to 81.4% and 95.3% of the benchmark set, respectively. The SARA server is freely accessible via the World Wide Web at http://sgu.bioinfo.cipf.es/services/SARA/.