e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation

Abstract

e-RNA offers a free and open-access collection of five published RNA sequence analysis tools, each solving specific problems not readily addressed by other available tools. Given multiple sequence alignments, Transat detects all conserved helices, including those expected in a final structure, but also transient, alternative and pseudo-knotted helices. RNA-Decoder uses unique evolutionary models to detect conserved RNA secondary structure in alignments which may be partly protein-coding. SimulFold simultaneously co-estimates the potentially pseudo-knotted conserved structure, alignment and phylogenetic tree for a set of homologous input sequences. CoFold predicts the minimum-free energy structure for an input sequence while taking the effects of co-transcriptional folding into account, thereby greatly improving the prediction accuracy for long sequences. R-chie is a program to visualise RNA secondary structures as arc diagrams, allowing for easy comparison and analysis of conserved base-pairs and quantitative features. The web site server dispatches user jobs to a cluster, where up to 100 jobs can be processed in parallel. Upon job completion, users can retrieve their results via a bookmarked or emailed link. e-RNA is located at http://www.e-rna.org.

Figure 1.

Arc plot visualising the predictions by the Transat web server. Each arc connects two positions that correspond to a base-pair and is coloured according to its estimated p-value, see legend in the top right. Solid arcs indicate arcs with mutually exclusive positions, while dashed arcs indicate those that overlap with an existing (and better) base-pair. Below the arcs, a covariance plot is shown, displaying the nucleotide of each sequence at each position. If two columns are base-paired and connected by a solid arc, we colour the two columns according to how conserved the base-pair is, green for fully conserved (no mutations), blue for compensatory mutations, and red for a loss of base-pairing.

Figure 2.

Pairing probability figure directly output from the RNA-Decoder web server, showing the probability of a single viral hairpin structure.