title: Web-Beagle: a web server for the alignment of RNA secondary structures.
abstract: Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods.
authors.affiliation: Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy.
authors.forename: Eugenio
authors.initials: E
authors.lastname: Mattei
authors.affiliation: Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Pietrosanto
authors.affiliation: Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 6, 40126 Bologna, Italy fabrizio.ferre@unibo.it.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Ferrè
authors.affiliation: Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy.
authors.forename: Manuela
authors.initials: M
authors.lastname: Helmer-Citterich
mesh_terms: D000465:Algorithms; D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA