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.
However, NCBI is phasing out GIs and we should instead use accession.version identifiers. I have downloaded those for my species, below is part of the file
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 :)
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