Question: How can I align two proteomes?
0
gravatar for lhernanj
11 months ago by
lhernanj0
lhernanj0 wrote:

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

protein alignment proteome • 255 views
ADD COMMENTlink modified 11 months ago by h.mon30k • written 11 months ago by lhernanj0

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

ADD REPLYlink written 11 months ago by Joe17k

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

ADD REPLYlink written 11 months ago by lhernanj0

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.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax85k

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"

ADD REPLYlink written 11 months ago by lhernanj0
0
gravatar for h.mon
11 months ago by
h.mon30k
Brazil
h.mon30k wrote:

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.

ADD COMMENTlink written 11 months ago by h.mon30k

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?

ADD REPLYlink modified 11 months ago • written 11 months ago by lhernanj0
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