Question: Visualization of protein similarity matrix
0
gravatar for jo.bac
2.6 years ago by
jo.bac0
jo.bac0 wrote:

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 !

alignment • 989 views
ADD COMMENTlink modified 2.6 years ago by h.mon31k • written 2.6 years ago by jo.bac0

maybe try calculating the manhattan distances and then MDS?

ADD REPLYlink written 2.6 years ago by egeulgen1000
0
gravatar for h.mon
2.6 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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.

ADD COMMENTlink written 2.6 years ago by h.mon31k
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