I have downloaded the NCBI nt database using the `blastdb_update.pl` perl script, but I want to blast some query file not on the whole nt database but on specific species. I know that when using blast locally it is possible to subset the nt/nr database using a list of GI identifiers, as explained [here][1]. 

However, [NCBI is phasing out GIs][2] and we should instead use accession.version identifiers. I have downloaded those for my species, below is part of the file `mygi.txt`.

When I run 

`blastdb_aliastool -gilist mygi.txt  -db nt -out sthg.out -title sometitle`

I obviously get 

`BLAST Database error: Specified file is not a valid GI/TI list.` since I am not providing a GI list.

I cannot find any command-line option in the manual to specify that I want to filter the nt database by accession number; any idea of how I can achieve that? I bet this option will have to be added by the BLAST team at some point :)

-----------------------
`mygi.txt` below

    AF324813.1
    AF324814.1
    AF324815.1
    AF324816.1
    AF324817.1
    AF324818.1
    AF324819.1
    AF324820.1
    AF324821.1
    AF324822.1
    AF324823.1
    AF324824.1
    AF370451.1
    AY198341.1
    AY198342.1


  [1]: https://www.biostars.org/p/6528/#6532%29
  [2]: http://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/
This solution adds a step but until NCBI updates the `blastdb_aliastool` to accept accession numbers this may the only way.

You can use `blastdbcmd` from blast+ package to retrieve sequences from `nt` db as fasta file followed by `makeblastdb` to make the blast indexes for the subset of sequences. my_acc.txt file is the file with accession numbers (one per line).

    blastdbcmd -db /path_to/nt -entry_batch my_acc.txt -out my_seq.fa