Hello,
I am creating a local nr blast database using the following command
makeblastdb -parse_seqids -dbtype 'prot' -in nr.fa -out nr -title nr -hash_index
it creates files like: nr.00.phd nr.00.phr nr.00.pog nr.00.psi nr.00.phi nr.00.pin nr.00.psd nr.00.psq
However, the files here ftp://ftp.ncbi.nlm.nih.gov/blast/db/ contain 3 extra files nr.00.pnd nr.00.pni nr.00.ppd
How to get these files? The reason I am asking is that sequence searching with my local version of nr is very slow. It takes >5 mins to blast a 400 amino acid protein against nr in a 32Gb machine with num_threads=5. Increasing mum_threads does not help. I am wondering if I am creating the database with wrong parameters. It takes <30 seconds in the ncbi portal
Please note: My use case does not allow me to download nr using update_blastdb.pl
