Best way to search for presence of gene in whole genome of related species
1
0
Entering edit mode
3.3 years ago
Mel161803 ▴ 10

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 bl2seq homologous gene • 590 views
ADD COMMENT
0
Entering edit mode
3.3 years ago
predeus ★ 1.8k

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 COMMENT

Login before adding your answer.

Traffic: 890 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