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?
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.