Of the three services, the RNAfold server provides both the most basic and most widely used function. Input consists of a single sequence that has to be typed or pasted into a text field of the input form.
In the simplest case, the server predicts only the minimum free energy (mfe) structure of a single sequence using the classic algorithm of Zuker and Stiegler (1
). In addition to mfe folding the server can calculate equilibrium base pairing probabilities via John McCaskill's partition function algorithm (4
By default the RNA energy parameters of the Turner group (13
) are used, but single stranded DNA sequences can be handled as well, by selecting the DNA parameter set provided by John SantaLucia (14
The fold server output consists of a static html page presenting the predicted mfe structure as a string in bracket notation and links to the plots generated for visualization. Three types of plots can be produced. Firstly, the predicted mfe structure is plotted as a conventional secondary structure graph using the naview layout method (15
). The pair probabilities can be visualized in a so-called ‘dot plot’: on a square grid of n
we draw for each possible pair (i
) a box with area proportional to its probability. Finally, we produce a mountain plot depicting both the predicted mfe and pair probabilities. A mountain plot is an xy
-graph that plots the number of base pairs enclosing a sequence position (for pair probabilities the average
number of enclosing pairs). See Figure for examples of all three representations.
Figure 1 Three representations for secondary structure and structure ensembles as produced by the RNAfold service: structure graph, mountain plot and dot plot. As can be seen clearly in the dot plot, the sequence has two almost equally good but very dissimilar (more ...)
Secondary structure drawing and dot plots are always produced in Postscript format. Postscript is used not only because it gives the highest print quality, but also because it allows the actual data to be embedded in the file, e.g. all pair probabilities are contained in the dot plot in an easy to parse format. On the other hand, Postscript files cannot be used for inline images on web pages and require additional software for viewing (e.g. gsview, http://www.ghostscript.com/
A suitable alternative is the new standard for Scalable Vector Graphics, SVG (http://www.w3.org/Graphics/SVG
). Users with SVG enabled browsers (typically through the use of Adobe's SVG plugin, http://www.adobe.com/svg/
) can request structure drawings in SVG, which allows some interactivity such as toggling annotation. Currently the server accepts sequences up to a maximum length of 4000
nt, sequences up to 300
nt will be processed immediately while longer jobs are submitted to a batch queue, in which case the user is notified by email after completion.