Welcome to MoSwA Documentation!
Motif SWitch Analyser is a tool that not only identifies all alignment k-mer positions that exhibit motif switching, but also provides a multi-faceted and extensive characterisation of the switches. This includes:
a short statistical summary on the switches observed;
an alignment view of all the switches observed in a given dataset, referenced against a consensus sequence built from the index sequences of the k-mer positions;
a network graph showing the dynamic interaction between the motif switches;
a bar plot showing clusters of motif switch positions, as well as hotspots in the protein alignment;
index switch positions are noteworthy and highlighted because highly conserved index at such positions are possibly to be avoided as vaccine targets given the instability of the index;
a pairwise alignment score based on PAM30 is provided for index switches, to determine the physico-chemical spectrum of similarity/variability between the index sequence and the replacing variant motif sequence.
You can simply upload your aligned file to MoSwA webserver which offers a simple and intuitive usage.
Check out the Usage section for further information, including how to Install Standalone version of MoSwA.