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.

Figure 1.

An example of the Web-Beagle output page. (A) Results page reporting a table containing all the computed pairwise alignments. Each row of the table contains the two input RNA ids and alignment statistics such as sequence and structural identity and similarity percentages. Moreover, z-score and p-value for the statistical evaluation of the alignment are displayed. Clickable column headings allow the user to sort the table by one of the parameters. By clicking on a row, the specific alignment for the selected pair of RNAs will be displayed (B). A color-coded representation for the alignment will help the user to identify aligned structural regions between the two RNAs. Along with the textual also a color-coded graphical representation will be displayed. Results can be exported as a flat file using the ‘download results’ button (b1).