Although SCANPS will read a normal FASTA formatted sequence file as the database to search, it runs more efficiently if you first build its own binary database files. This is particularly important for the MMX/SSE versions of the program. SCANPS is used to build its own databases. For example:
scanps -mode 99 -d trembl.fa -bdb trembl
will take a FASTA formatted sequence database file called ``trembl.fa'' and create the SCANPS binary database and index files ``trembl.bix'' and ``trembl.bsq'' in the directory /db/scanps (or whatever you specified in the scanps_defaults.dat file above.
Once you have your binary database file and a sequence you want to scan you specify the two on the command line - e.g.:
scanps -s test.fa -bdb trembl > test_trembl.log
the output of the scan is written to standard output which in this case is redirected to the file test_trembl.log.