Visualization of protein similarity matrix

Question

[jo.bac]

Hello ! I have a protein similarity matrix created from an MSA by scoring 1 if the AA is the same and 0 otherwise. I would like to visualize groups in this matrix, but I am not sure which method to use. Should I use MDS,PCA,clustering... ? I am not sure that the matrix I have can be converted into a true distance metric. Also, it is pretty big (20000*20000) so this complicates things.

Thank you very much for your suggestions !

[egeulgen]

maybe try calculating the manhattan distances and then MDS?

Answer 1

[h.mon]

I have a protein similarity matrix created from an MSA by scoring 1 if the AA is the same and 0 otherwise.

Why are you ignoring decades of research and knowledge? Do you have a good reason to use this scoring system?

Here is one answer to get a true distance matrix: Question: Any tool to generate protein similarity matrix.