01599nas a2200145   4500008004100000245006100041210006000102300001100162520114400173653000801317653001801325100002201343700002401365856006401389       2009                        eng d00aSARA: a server for function annotation of RNA structures0 aSARA a server for function annotation of RNA structures  agkp4333 a<p>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/.</p>10aRNA10aRNA structure1 aCapriotti, Emidio1 aMarti-Renom, M., A.  uhttp://nar.oxfordjournals.org/cgi/content/abstract/gkp433v1