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Excluding environmental sequences with blastn command line

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

blast
• 4,497 views • link
updated by Ram Ram • written by FC • FC

1 answer

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

• 1 views • link
written by Ram Ram

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

• 1 views • link
updated by Ram Ram • written by FC • FC

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.

• 1 views • link
written by Ram Ram

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