Question: Phylogenetic Profile Matrix
0
gravatar for ewre
5.1 years ago by
ewre220
United States
ewre220 wrote:

Hi all,

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

• 1.4k views
ADD COMMENTlink modified 5.1 years ago by Asaf5.3k • written 5.1 years ago by ewre220
0
gravatar for Asaf
5.1 years ago by
Asaf5.3k
Israel
Asaf5.3k wrote:

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.

ADD COMMENTlink written 5.1 years ago by Asaf5.3k

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?

ADD REPLYlink written 5.1 years ago by ewre220

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.

ADD REPLYlink written 5.1 years ago by Asaf5.3k

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

ADD REPLYlink written 5.0 years ago by ewre220

Number of representatives of the COG group in the genome

ADD REPLYlink written 5.0 years ago by Asaf5.3k
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