search

agartland / palmotif

Python package for computing and plotting sequence logos, with output as SVG or matplotlib
MIT License
2 stars 1 forks source link

missing value in sequence #3

Open SheahLinLee opened 2 years ago

SheahLinLee commented 2 years ago

Hi,

I have a set of peptide sequence but some of them have missing value such as "AMRE*NSGYSTLT". Is there a way to deal with this to include them in the motif?

Thank you.

agartland commented 2 years ago

Yes. When computing the motif you will need to ensure that '*' is part of your alphabet (see compute_motif).

This can be a little trickier if you are trying to compute a motif that requires alignment since then the new character also must be given substitution values in the matrix (see compute_pal_motif).

You could also consider replacing the * with a gap or some other AA. You may also consider not including these sequences in your motif if they have a stop codon or something else that makes them biologically implausible. Hope that helps!