Question: IceLogo Plots for Python or R
0
gravatar for eneskemalergin
11 months ago by
Canada/Vancouver/UBC
eneskemalergin10 wrote:

Hello all,

I need to plot IceLogo's of the peptide sequences, to show their values corresponding to the expected values. The only option that I could find until this point is iceLogo, which is written in Java and has a web server too. However the web server doesn't work sometimes. The standalone package, on the other hand works but doesn't accept multiple plots at the same time. So what I am asking is if there is a package or scripts out there written in Python or R to plot IceLogos, so that I don't have to re-invent the wheel. Another reason I am looking for R or Python script is that I would like to add this into our proteomics workflow.

Thank you.

R visualization python • 500 views
ADD COMMENTlink modified 11 months ago by Hussain Ather890 • written 11 months ago by eneskemalergin10

Specifically iceLogos or any logo?

ADD REPLYlink written 11 months ago by jrj.healey9.1k

Yes, iceLogo because they provide more information in the plot that logo is shown. "While an iceLogo has a lot in common with sequence logos, especially visually, it has a number of advantages. It will always use a reference set, and it allows for changing the scoring system used." [1]

1 - http://iomics.ugent.be/icelogoserver/manual#icelogo

ADD REPLYlink written 11 months ago by eneskemalergin10
0
gravatar for Hussain Ather
11 months ago by
Hussain Ather890
National Institutes of Health, Bethesda, MD
Hussain Ather890 wrote:

Have you tried peptide-sequence-alignment ?

ADD COMMENTlink written 11 months ago by Hussain Ather890
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