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/.

Capriotti, E., Marti-Renom, M.A. (2009). SARA: A server for function annotation of RNA structures. NUCLEIC ACIDS RESEARCH, 37(SUPPL. 2), W260-W265 [10.1093/nar/gkp433].

SARA: A server for function annotation of RNA structures

CAPRIOTTI, EMIDIO;
2009

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/.
2009
Capriotti, E., Marti-Renom, M.A. (2009). SARA: A server for function annotation of RNA structures. NUCLEIC ACIDS RESEARCH, 37(SUPPL. 2), W260-W265 [10.1093/nar/gkp433].
Capriotti, Emidio; Marti-Renom, Marc A
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11585/564922
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