How can I align two proteomes?

Question

[lhernanj]

Hello all, I want to align two complete proteomes, not proteins. I was thinking to try "proteny" but my proteomes are from bacteria and proteny was used to eukaryotes so I do not know if it is correct to use proteny.

Does anybody know how to do that?

thanks in advance

[Joe]

Sorry, what do you mean by “aligning proteomes” if not aligning protein sequences?

[lhernanj]

align all proteins of a strain against all proteins of another strain to get the synteny, that is the objective

[GenoMax]

my proteomes are from bacteria and proteny was used to eukaryotes

Should that matter? All proteny seems to need is following:

a genome FASTA file and a GFF3 file of genes for each genome that you wish to use.

[lhernanj]

I am not sure if that is important but the point is that I did not find any study which uses proteny with prokaryotes and furthermore it was design to detect clusters of "exons"

Answer 1

[h.mon]

You don't describe your data in detail, so I will assume you want to find the orthologous proteins between two protein sets. There are many pipelines for this task, for the good old OrthoMCL to more recent implementations like OMA or Proteinortho.

[lhernanj]

My data are all proteins of a strain and all proteins of another strain. I was looking at Proteinortho and I am going to try it because it seems that I need. However, what software could I use to draw the synteny after using Proteinortho?