filter NCBI-NR “non-redundant” protein database

Question

[PolDE]

Dear All,

is it possible to download the NCBI-NR “non-redundant” protein database based on taxa assignment; for example nr accessions only for virus taxa, avoiding download of the whole database.

Thanks a lot

[GenoMax]

No there is no way to selectively download a part of the pre-formatted nr database. But you can filter your results using taxid limit options.

[PolDE]

ok thanks, how do I filter afterwards

[GenoMax]

You can filter the results using one of the following (there are additional options you can look at using in-line help) (you would still need the full nr db):

 -taxids <String>
   Restrict search of database to include only the specified taxonomy IDs
   (multiple IDs delimited by ',')
    * Incompatible with:  gilist, seqidlist, taxidlist, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_lo

 -taxidlist <String>
   Restrict search of database to include only the specified taxonomy IDs
    * Incompatible with:  gilist, seqidlist, taxids, negative_gilist,
   negative_seqidlist, negative_taxids, negative_taxidlist, remote, subject,
   subject_loc