**20**wrote:

Is there a way to compute a distance between two PWMs using a substitution matrix? (for genes, prots or arbitrary alphabets doesn't matter)

Say I have PWM1 corresponding to a Motif in a certain set

PWM2 is the same for another dataset

I have a substitution matrix of the alphabet I am using

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What are the possibilities to compute a distance between those two?

**21k**• written 4.6 years ago by marco23.p •

**20**