Best DB format for fastest FASTA search?

Dr. Greg Quinn greg at
Thu Dec 30 18:07:53 EST 1999

William R. Pearson (wrp at wrote:
: 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.
: Bill Pearson

Thanks for this information and explanation.

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