Couple days ago, I used nucleotide seqs from JGI website and had to create my own blast database. Before I do that, I had to get rid of some of the extra defline info that makes sense only for JGI. I did it with VIM editor
Usage:
%s/search_pattern/replace_pattern/g
Example:
%s/jgi|Poptr1_1|[0-9]*//g
Enjoy!