Question: how to find an ortholog of a protein of interest from a full genome sequence of a bacteria?
0
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19 months ago by
researcher0
researcher0 wrote:

hi I am a newbie trying to find a ortholog of a protein that I am interested in from a full genome sequence of a bacteria. I tried this and that (BLAST, etc) but could not figure out how to do this. could anyone help me?

I have a protein, I know the sequence of couple ortholog of the protein from different bacterial strains. I have a full genome sequence of a bacteria where I am trying to find the ortholog of the protein I am interested in.

any help is appreciated. Thanks alot!

ortholog • 520 views
ADD COMMENTlink modified 19 months ago by h.mon29k • written 19 months ago by researcher0

you can use also orthofinder or orthomcl...for that

ADD REPLYlink written 19 months ago by kamel30
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19 months ago by
h.mon29k
Brazil
h.mon29k wrote:

Quick and dirty method:

  1. If the genome you have is not annotated, annotate it (locally with Prokka, or remotely with RAST).

  2. Create a blast database with the predicted proteins.

  3. Blast the "couple ortholog of the protein" against this blast database, find the best high similarity hits.

ADD COMMENTlink written 19 months ago by h.mon29k
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