Plotting sequence similarity/identity of a multiple sequence alignment

Question

[Adrian Pelin]

Hello,

I have multiple sequence alignment files, some of NT some of AA. I wanted to plot similarity of these alignments along the coordinates of the alignment.

Basically the alignment should highlight regions that are very conserved among sequences and regions that are very divergent.

Something similar has been achieved here:

http://www.biology.wustl.edu/gcg/figure/plotsimilarity_1.gif

I am having no luck finding this in google.

Thanks, Adrian

[zizigolu]

http://wiki.c2b2.columbia.edu/workbench/index.php/Pattern_Discovery has something about similarity, or Cytoscape worm plot

Answer 1

[GenoMax]

PlotSimilarity from GCG .. brings back memories.

You could use plotcon from EMBOSS as a replacement: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/plotcon.html

Dot plots may also be an alternative.

[Adrian Pelin]

Brilliant! This works perfectly.