how to visualizing residue wise pairwise protein alignment

Question

[kng]

How can I visualize the similarity percentage per residue for results from pairwise sequence alignment (results from emboss water). I would like each residue of my query protein sequence in x axis and percentage similarity to the target in y axis.

[GenoMax]

Use one of the options in EMBOSS: https://emboss.sourceforge.net/apps/cvs/emboss/apps/alignment_dot_plots_group.html

[kng]

hi GenoMax , what I want is more like what is done here http://rothlab.ucdavis.edu/genhelp/plotsimilarity.html . But I am not able to reproduce this. Are there similar tools to plot similarity score per residue ?

Answer 1

[GenoMax]

Then you probably want plotcon: https://emboss.sourceforge.net/apps/release/6.0/emboss/apps/plotcon.html