Question: How to calculate the mutual information (MI) between two sites on a protein sequence?
0
gravatar for Bjoux
7 days ago by
Bjoux0
China/Changsha/CSU
Bjoux0 wrote:

How to calculate the mutual information (MI) between two sites on a protein sequence? what I need is a standalone tool or python script. Thanks.

mutual inforamtion • 139 views
ADD COMMENTlink modified 7 days ago by Jean-Karim Heriche13k • written 7 days ago by Bjoux0

I don’t really understand what you mean by mutual information? Can you elaborate?

ADD REPLYlink written 7 days ago by jrj.healey2.8k
3
gravatar for Jean-Karim Heriche
7 days ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche13k wrote:

Mutual information is a concept from information theory that aims at quantifying how dependent two variables are. On multiple sequence alignments, it can be used to identify co-evolving sites and can be computed from the column entropy. This paper may be relevant. MI for alignments can be computed with the R package BioPhysConnectoR

ADD COMMENTlink written 7 days ago by Jean-Karim Heriche13k

Ah OK, I wasn't sure if it was an actual term or not but guessed it would probably be related to the column entropy.

ADD REPLYlink written 5 days ago by jrj.healey2.8k
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