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

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 align-ments, Transat detects all conserved helices, includ-ing those expected in a final structure, but also tran-sient, 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 si-multaneously co-estimates the potentially pseudo-knotted conserved structure, alignment and phy-logenetic tree for a set of homologous input se-quences. 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 visu-alise RNA secondary structures as arc diagrams, allowing for easy comparison and analysis of con-served 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 a