This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Best way to search for presence of gene in whole genome of related species

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
• 1,254 views • link
updated by predeus predeus • written by Mel161803 • Mel161803

1 answer

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.

• 0 views • link
written by predeus predeus

Log in to answer this question.

More posts like this