SwiSpot is a command-line utility for predicting riboswitch alternative configurations. It is based on the prediction of the so-called switching sequence, to subsequently constrain the folding of the two functional structures. While in principle it can find out different switching behaviours, currently SwiSpot is able to classify only riboswitches (without pseudoknots) that rely on transcription termination via terminator hairpins, or translation inhibition via SD sequestering/releasing.

The description of the SwiSpot methodology and tool is available on:
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw401

Download and installation

SwiSpot can be downloaded in both Python and C versions. Please refer to the menu on the left.
Installation instructions are provided as well.