Question: how to find an ortholog of a protein of interest from a full genome sequence of a bacteria?
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gravatar for researcher
9 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 • 296 views
ADD COMMENTlink modified 9 months ago by h.mon26k • written 9 months ago by researcher0

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

ADD REPLYlink written 9 months ago by kamel20
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9 months ago by
h.mon26k
Brazil
h.mon26k 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 9 months ago by h.mon26k
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