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.



The following individuals have contributed code to MoSwA:

  • Muhammet Celik

  • Shan Tharanga

  • Kaushal Kumar Singh

  • Mohammad Asif Khan