public class PRISM
extends java.lang.Object
This is a simple commandline driver for PRISM. It presents a clean interface that requires the user to submit a fasta file, but allows
him or her to specify a different background sequence. Only one final file is created, and this file may be specified by the -o option.
Optionally, the user can supply a motif, and this driver will report all the instances of the motif in the fasta sequences. The only
parameter of any substance is the option to turn off filtering (by default, the final results are filted for overlaps in the given fasta
files). Options can be found by using the -h flag.