I'm doing some local BLASTS with BLAST+ v2.10.1 and was wondering if anyone could tell me what the database files actually are/do - they are made using makeblastdb with a fasta file and the suffixes are: .pdb, .phr, .pin, .pot, .psq, .ptf, .pto.
Also, I assume BLAST+ does this automatically, but is there any way to speed up blast using these? I currently just set the database as whatever the file name is up to the suffix above - so for example, if I have files mydb.pdb, mydb.phr, mydb.pin, mydb.pot, mydb.psq, mydb.ptf and mydb.pto, I will set the database flag as 'file/path/to/mydb' (with no suffix). Is there any way to use these files to speed up the BLAST search (e.g. with one of the many blast cmd flags) or does BLAST do this all as fast as possible automatically?
Perfect, thanks for the answer!