The most efficient formats for fasta to read are FASTA format,
BLAST2.0 format, and compressed GCG format. If you are doing several
successive searches and have a fair amount of memory, you should run
the "map_db" program for FASTA and compressed GCG files to create an
index (.xin) file, which allows the database to be memory mapped.
Memory mapping improves database reading efficiency substantially
(reducing search time as much as 33%) the first time the database is
searched, and even more dramatically subsequently (if the database
remains memory mapped).
Memory mapping is available in fasta32 and fasta33.