Excluding environmental sequences with blastn command line

Question

[FC]

Dear community,

In blast webpage we can choose to exclude environmental and uncultured sequences. How can we do that with blastn command line?

I apologize if this is a simple question, but I'm starting to use blastn and didn't found the solution for this anywhere.

Thanks in advance,
Francisco

Answer 1

[Ram]

I think you may have to create a list of GIs that fall under ENVIRONMENTAL and UNCULTURED categories and use it in the -negative_gilist argument to blast.

Source: http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.Query_a_BLAST_database

[FC]

Thank you for your answer Ram. Any suggestion on how to do that? Sorry, don't want to post a "give me the code question", but I'm just starting now with blastn.

Cheers,
Francisco

[Ram]

I'm not really sure. From the static nature of the options in there, I'm guessing quite a bit of work went into figuring out these GIs. Maybe grepping the base set of sequences for headers containing these words will prove to be a possible lead.

[FC]

I searched a little more and found this post - Running Blastn Locally: Exclude Uncultured Sequences. Thank you for your help Ram!

Francisco