which python graphics library for plotting protein sequence data
Entering edit mode
14 months ago
The ▴ 180

I'll have to code in PYTHON some visualization method for multiple protein sequences and subsequences. I would try to show the alignment of many fragment sequences to the original sequences showing the position of fragments and the amino acids. The amino acids are to be colored by some physico-chemical properties.Something similar but not exactly the pic. as this:

enter image description here

Can somebody recommend any graphics or other library in Python suitable for this kind of job? The output can be graphics file like png or interactive graphics or html, doesn't matter really for me.

Thanks in advance

python data sequence visualization protein • 423 views
Entering edit mode

Hm, you could probably try to play with bash colored printing, but beware the usefulness of a bash alignment visualization to cite this towardsdatascience blog post:

After the alignment is done, you can visually inspect it with one of many alignment viewers. Unfortunately, this is not a process easily done from the command line, so Biopython doesn’t try to give you that ability.

Maybe less -rS ??

Entering edit mode

unfortunately I'm expecting my data format will be different from standard alignment formats and may not work with the common alignment viewers


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