Many examples can be found in the man pages. This page will be updated with additional examples.
These files may be used to try the examples below
example.modmodstorm -B -w 250 -f -t 0.90 -H gk-table \ -s example.faa example.modReports all occurrences of the module example.mod in example.faa , with the individual motif thresholds set to a functional depth of 0.90, and all motifs occurring in a window of 250 bases. The -B flag indicates that sites in the module are allowed to occur on either strand.
modstorm -O -H gk-table -s example.faa \ example.modReports all occurrences of the module example.mod in example.faa that occur with the organization as specified in example.mod
modstorm -NO -H gk-table -s example.faa \ example.modThis is the same as Example 2 except the searching is done without preprocessing the sequences into suffix trees.