how to find an ortholog of a protein of interest from a full genome sequence of a bacteria?
1
0
Entering edit mode
3.0 years ago
researcher • 0

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 • 788 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
3.0 years ago
h.mon 33k

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 COMMENT

Login before adding your answer.

Traffic: 1723 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6