blastdb_aliastool mismatch converted GIs and final sequences

Question

[roger.huerlimann]

Hi all,

I followed this advice to subset the nr database with a specific taxonomic group: Vertebrate Subset Nr Database? Build My Own?

However, even though there were about 5 million GIs, the resulting database only ended up being 2 million sequences. Is this working as intended? Both the nr database and the GIs have been downloaded with only a day between, so I don't think someone placed 3 million sequences within that time period.

>blastdb_aliastool -gilist virus.gi_list180712.txt -db nr -out nr_virus -title nr_virus
Converted 4764026 GIs from virus.gi_list180712.txt to binary format in nr_virus.p.gil
Created protein BLAST (alias) database nr_virus with 2239853 sequences

Thanks!

Roger

[GenoMax]

@Roger: NCBI deprecated gi's for outside use a couple of years back. You could use all the viral genomes here or get the sequences for taxID you want using NCBI eUtils.