Paper Info
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.
Year
DOI
Venue
2015
10.1093/nar/gkv489
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
RNA,Structural alignment,Biology,Artificial intelligence,Nucleic acid secondary structure,Sequence alignment,Pairwise comparison,Pattern recognition,Smith–Waterman algorithm,Bioinformatics,Genetics,Substitution matrix,Web server
Journal
43
Issue
ISSN
Citations 
W1
0305-1048
2
PageRank 
References 
Authors
0.37
12
4
Name
Order
Citations
PageRank
Eugenio Mattei120.37
Marco Pietrosanto220.71
F Ferrè319019.97
Manuela Helmer-Citterich4161.18