I have downloaded and format (makeblastdb) the nr database from NCBI for my own local database (February 2017) . I want to extract subset from the nr database.
I have tried below method:
- Download GIlist from NCBI
- Use blastdb_aliastool to extract the subset.
Above method worked well for older database (2013) but show error "BLAST Database error: GI list specified but no ISAM file found for GI" for my recently download database. My understanding is NCBI no longer support GI.
I have also tried download target sequences as fasta file from NCBI directly as shown in http://www.ionsource.com/tutorial/db/tips_for_creating_species_specif.htm but download seem to be failed every time before complete.
Any other suggestion? I need to download nr database for txid5204[ORGN].