e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features

Abstract

e-RNA is a collection of web-servers for the prediction and visualisation of RNA secondary structures and their functional features, including in particular RNA-RNA interactions. In this updated version, we have added novel tools for RNA secondary structure prediction and have significantly updated the visualisation functionality. The new method CoBold can identify transient RNA structure features and their potential functional effects on a known RNA structure during co-transcriptional structure formation. New tool ShapeSorter can predict evolutionarily conserved RNA secondary structure features while simultaneously taking experimental SHAPE probing evidence into account. The web-server R-Chie which visualises RNA secondary structure information in terms of arc diagrams, can now be used to also visualise and intuitively compare RNA-RNA, RNA-DNA and DNA-DNA interactions alongside multiple sequence alignments and quantitative information. The prediction generated by any method in e-RNA can be readily visualised on the web-server. For completed tasks, users can download their results and readily visualise them later on with R-Chie without having to re-run the predictions. e-RNA can be found at http://www.e-rna.org.

Graphical Abstract

e-RNA contains a collection of web tools for predicting RNA secondary structure features. The R-Chie server allows users to create a variety of visualisations of RNA secondary structure or RNA-RNA interactions.

Figure 1.

Experimentally confirmed case of co-transcriptional folding. We can observe three possible RNA secondary structures formations coloured differently and multiple sequence alignment annotation for one of the structures.

Figure 2.

Example of ShapeSorter prediction for SAMI riboswitch of T.Tengcongensis organism. Arcs are coloured by p-value of prediction, and the graph with a line underneath arcs shows binned SHAPE reactivity values, obtained by ShapeSorter pre-processing. Maximum is 5 and -1 stands for the absence of SHAPE value for nucleotide position, bars are coloured based on the value of reactivity (yellow is 0 and red is 5, black is the absence of SHAPE reactivity value).

Figure 3.

Example of RNA–RNA interactions. Here we can observe ‘CyaR’ sRNA at the bottom of the figure, and its known target mRNAs (luxS,nadE,ompX,yqaE) at the top of the figure. Arcs are showing cis interactions while lines show trans interactions (54).

Figure 4.

Short RNA structure feature overlapping one 3’ splice site in M segment of influenza A. Arcs are coloured based on prediction p-value. Top arcs are related to the Human secondary structure and the bottom is to Avian secondary structure (53).