Web-Beagle: a web server for the alignment of RNA secondary structures

• Published in: Nucleic acids research Vol. 43; no. W1; pp. W493 - W497
• Main Authors: Mattei, Eugenio, Pietrosanto, Marco, Ferrè, Fabrizio, Helmer-Citterich, Manuela
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2015
• Subjects: Algorithms; Internet; Nucleic Acid Conformation; RNA - chemistry; Sequence Alignment; Sequence Analysis, RNA; Software; Web Server issue
• ISSN: 1362-4962; 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkv489

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.