For some softwares I have had to index a reference genome prior to using blastn. Here is an example command:
makeblastdb –in mydb.fsa –dbtype nucl –parse_seqids
Whenever I do this I retain the original fasta file plus a bunch of extra files made by the command. For example:
mydb.nhr, mydb.nin, mydb.nsd, mydb.nsi, etc.
I haven't found very clear documentation as to what is happening with this command and what file is the final indexed genome that I should be using. Any links, information, or explanation on this is greatly appreciated.
BLAST Command Line Applications User Manual