title: Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package.
abstract: BACKGROUND
  Aligning RNAs is useful to search for homologous genes, study evolutionary relationships, detect conserved regions and identify any patterns that may be of biological relevance. Poor levels of conservation among homologs, however, make it difficult to compare RNA sequences, even when considering closely evolutionary related sequences.
  
  
  RESULTS
  We describe SARA-Coffee, a tertiary structure-based multiple RNA aligner, which has been validated using BRAliDARTS, a new benchmark framework designed for evaluating tertiary structure-based multiple RNA aligners. We provide two methods to measure the capacity of alignments to match corresponding secondary and tertiary structure features. On this benchmark, SARA-Coffee outperforms both regular aligners and those using secondary structure information. Furthermore, we show that on sequences in which <60% of the nucleotides form base pairs, primary sequence methods usually perform better than secondary-structure aware aligners.
  
  
  METHODS
  The package and the datasets are available from http://www.tcoffee.org/Projects/saracoffee and http://structure.biofold.org/sara/.
authors: Bioinformatics and Genomics Program, Centre for Genomic Regulation, 08003 Barcelona, Spain.
authors: Carsten
authors: C
authors: Kemena
authors: Giovanni
authors: G
authors: Bussotti
authors: Emidio
authors: E
authors: Capriotti
authors: Marc A
authors: MA
authors: Marti-Renom
authors: Cedric
authors: C
authors: Notredame
mesh_terms: D000465:Algorithms; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA