*This is a beta version of the ScanFold web server. Help us improve the service by sending any feedback to wmoss@iastate.edu. Thanks!* UPDATE! Read more about the ScanFold webserver, described in detail here: Methods paper
Using the ScanFold web server you can identify regions within large RNA sequences which generate unusually stable secondary structures (one of the hallmarks of a functional RNA). Read more about
The results of ScanFold are output directly to an embedded igv.js browser as well as downloadable text files. Only the most significant base pairs (as determined by their z-scores) are depicted directly on the browser as arcs, and base pairs which contributed to particularly unusual (potentially functional) structures are colored blue (yellow and green are less favorable, and grey base pairs were from structures no more stable than random). In the example below, we simply input the region of the human VEGFA mRNA three prime UTR known to contain a functional RNA secondary structure: a riboswitch. The blue base pairs (considered most significant) match the previously described model of the riboswtich.
Below each base pair (or unpaired nucleotide) are the average z-scores (Zavg) from the windows in which they appeared. Details about the z-score and other metrics can be found below; briefly however, more negative z-scores suggest a higher likelihood of functionality, and in the example above, highly negative Zavg base pairs, are derived from a known functional RNA. Details about interpreting results can be found in the user guide below.
ScanFold User Guide (PDF)
