Visualize or plot protein architecture (regions/domains) using the position of amino acids

Question

[anioannides6]

Hi all,

I have the following table(s) (showing a part here), where the position of aminoacid is shown in column 1 and the type (1 for lcr, -1 for disorder) is shown in column 2:

#AA Type
6     1
10    1
11    1
14   -1
15   -1

I would like your opinions on how to visualize this kind of data. Each table is for a single protein. My idea is to create something like a plot, showing the protein length, both the LCR and disorder regions, and also the consensus. My tables are very large in size and I would prefer the process to be done using a script. Can this be done in R? If yes any suggestions on how to do this? If not, what's the most efficient way of doing it?

Edit: a linear overview is preferred! (shown below) IMAGE Thanks

Answer 1

[Ibrahim Tanyalcin]

Dear,

I have written a software that does this kind of visualization. It adopts a circular format because rectangular windows do not give complete overview at glance. You can upload your custom files if you like. Try the below example and see if it fits your needs:

http://i-pv.org/EGFR.html

I recommend google chrome/safari or firefox.

[anioannides6]

Thanks, I'll check it out. Although I prefer a linear overview like:

[Ibrahim Tanyalcin]

Dear,

Sure try both representations and choose what fits you best. If your focus will be on the amino acid composition/mutations and residue based features a circular representation will fit more since it makes better use of space.

However if you want to compare domains between different proteins a rectangular view with windows can be more useful.

Good luck!