Build substitution matrix for protein alignment

Question

[nitrushina]

Hello! Does anyone know of a script or programme to build a matrix based on alignment of 2 or more proteins? I would like to have something like a table where for each amino acid or gap in row there is a number of how many times it changed to the one in column. Thank you in advance

[lieven.sterck]

What have you tried so far? have you tried googling for it? here are a number of biostar post on the same/similar topic (found by searching for it):

Make matrix of protein pairwise identities/similarities from multiple protein sequences

Position Weight Matrix From Sequence Alignment

How do I generate a character state matrix?

[nitrushina]

Thank you! It is the variation of character state matrix I was looking for. No need to be rude, of course I googled for it, just couldn't find the right words apparently, my bad.

[Kevin Blighe]

I see absolutely nothing in lieven.sterck's comment that could be construed as rude

[nitrushina]

Maybe, but from my perspective it always sounds condescending when people ask if the questioner was googling for it. Of course they did. I personally spend a lot of time trying to figure a solution on my own and only then ask someone.

[lieven.sterck]

experience tells us that often people did not take the effort of first doing a small query on google before they post here. (also the links I provided where simply exemplary and by far not exhaustive). I apologise if you were addressed unrightfully.

anyway, let's keep a constructive mindset here: Perhaps you need to/can elaborate a little more on the specifics of your question/problem.

Answer 1

[nitrushina]

So I made a replacement dictionary as described in one of the answers here: Creating your own substitution matrix from an alignment and then on its base I built a matrix where the substitutions like A->T and Y->A are counted as separate. Because SubsMat module seems to only allow you to build symmetrical matrices where the direction of change doesn't count.