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Standalone blast / command line blast

I am trying to blast some of the sequences in the standalone blast. The problem I am facing is that, I am getting hits against the uncultured bacteria. Is there any flags to exclude the uncultured or environmental samples from the command line blast results as we can do in the blast website. Any solution would be highly appreciated.

blast
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updated by Petr Ponomarenko Petr Ponomarenko • written by vishwaas1704 • vishwaas1704

edited from "tool" to "question".

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written by h.mon h.mon

You should look into customizing your local database.

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written by st.ph.n st.ph.n

What database are you using for the search?

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written by GenoMax GenoMax

1 answer

you can use negative gi list as shown in https://www.ncbi.nlm.nih.gov/books/NBK279679/

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written by Petr Ponomarenko Petr Ponomarenko

GI numbers are history and are not an option any more. I don't recollect if NCBI has updated BLAST+ to use accession numbers instead.

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written by GenoMax GenoMax

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