William R. Pearson (wrp at alpha0.bioch.virginia.edu) 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.