IceLogo Plots for Python or R

Question

[eneskemalergin]

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.

[Joe]

Specifically iceLogos or any logo?

[eneskemalergin]

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

Answer 1

[Hussain Ather]

Have you tried peptide-sequence-alignment ?