Question: Best way to search for presence of gene in whole genome of related species
gravatar for Mel161803
14 months ago by
Mel16180310 wrote:

I've been trying to check for the presence/absence of homologous genes in bacteria species closely related to my bacteria of interest using blast 2 sequences from NCBI, using tBLASTx. I was told that this is not the best way, and that I should annotate the whole genomes that I have, and then compare the two proteins directly. However this is rather complicated, and takes a lot of time. Is there any easier method?

blast homologous gene bl2seq • 238 views
ADD COMMENTlink modified 14 months ago by predeus1.4k • written 14 months ago by Mel16180310
gravatar for predeus
14 months ago by
predeus1.4k wrote:

Annotating the whole genome for your purposes is not that hard - it's now routinely done by Prokka. If you want to analyze presence/absence of particular genes, just do the following:

  • run Prokka on all genomes you have;
  • run Roary on the GFF files produced by Prokka

This is pretty much it - you'll get a table with gene presence/absence etc.

ADD COMMENTlink written 14 months ago by predeus1.4k
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