title: SARA: a server for function annotation of RNA structures.
abstract: 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/.
authors.affiliation: Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.
authors.forename: Emidio
authors.initials: E
authors.lastname: Capriotti
authors.forename: Marc A
authors.initials: MA
authors.lastname: Marti-Renom
mesh_terms: D000465:Algorithms; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods; D012984:Software
chemical_list: D012313:RNA