About ScanFold

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Welcome to the ScanFold web server

ScanFold results for the COVID-19 strain (SARS-CoV-2) can be found on the RNAStructuromeDB: here.

*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).

The underlying ScanFold algorithm was originally described here (where example uses and verifications are demonstrated): ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV. Simply input an RNA sequence into the ScanFold (Full Pipeline) server to map its structural landscape and identify uniquely stable RNA secondary structures.

Each of the subroutines comprising ScanFold have also been given separate servers:

1. ScanFold-Scan runs a scanning window analysis on an input sequence

2. ScanFold-Fold takes the results of a scanning window analysis (e.g. the output of ScanFold-Scan; see ScanFold User Guide for details on formatting scanning window analysis results from other programs to be used with ScanFold-Fold) and identifies the individual base pairs which contributed most to low z-score windows.