Phylogenetic Profile Matrix

Question

[ewre]

Hi all,

How can I get a gene phylogenetic profile matrix which contains present/absent information of genes in a handful of species?

Answer 1

[Asaf]

You can download one from STRING database.
Choose Download on top and download the file species.mappings.v9.1.txt.gz you can pretty easily generate a matrix from this file.

[ewre]

Hi Asaf, I have downloaded the file you mentioned above, It has 3 columns, but I cann't figure out how to generate the matrix. can you provide some clues to do this?

[Asaf]

The first column is taxonomy ID, the second is group of proteins and the third the number of representatives of the group in the genome. You can convert it pretty easily to a matrix form by putting True in the matrix where the TXID and the protein family appear in a row and False otherwise. You should need to program a bit.

[ewre]

I got the idea. what does the third column exactly mean in this table?

[Asaf]

Number of representatives of the COG group in the genome