Standalone blast / command line blast

Question

[vishwaas1704]

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.

[h.mon]

edited from "tool" to "question".

[st.ph.n]

You should look into customizing your local database.

[GenoMax]

What database are you using for the search?

[vishwaas1704]

i am using the NCBI's nt database

Answer 1

[Petr Ponomarenko]

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

[GenoMax]

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.

[Petr Ponomarenko]

Agree. Nonetheless, history of databases and tools is maintained. We still use ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.3.0/ sometimes. It had GI support.