Good morning, I'm aligning with blast some species, against all nt database to analyse the vegetables. However, in some cases we have species of animals mixed with vegetables and want only to detect the vegetable species. Normally, we would only expect to detect the vegetables only. But this is normal since we are using the all nt. So now, could anyone point me out, the way to detect only vegetables? Thanks for the help.
Using the blast command line tool, you can limit your search to a specific taxon using the
So, in your case
-taxids 3193 should limit your search to plants.
If you are using the ncbi blast webinterface, you can restrict your search by entering "plants" into the Organism field in the "Choose Search Set" section