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.

Mattei, E., Pietrosanto, M., Ferrè, F., HELMER CITTERICH, M. (2015). Web-Beagle: a web server for the alignment of RNA secondary structures. NUCLEIC ACIDS RESEARCH, 43(W1), 493-497 [10.1093/nar/gkv489].

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

HELMER CITTERICH, MANUELA
2015

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.
Pubblicato
Rilevanza internazionale
Articolo
Esperti anonimi
Settore BIO/11
English
Con Impact Factor ISI
http://nar.oxfordjournals.org/content/early/2015/05/14/nar.gkv489.long
Mattei, E., Pietrosanto, M., Ferrè, F., HELMER CITTERICH, M. (2015). Web-Beagle: a web server for the alignment of RNA secondary structures. NUCLEIC ACIDS RESEARCH, 43(W1), 493-497 [10.1093/nar/gkv489].
Mattei, E; Pietrosanto, M; Ferrè, F; HELMER CITTERICH, M
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2108/112891
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