modstorm examples

Example files

These files may be used to try the examples below

example.mod
example.faa

Example 1

modstorm -B -w 250 -f -t 0.90 -H gk-table \
-s example.faa example.mod

Reports 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.

Example 2

modstorm -O -H gk-table -s example.faa \
example.mod 

Reports all occurrences of the module example.mod in example.faa that occur with the organization as specified in example.mod

Example 3

modstorm -NO -H gk-table -s example.faa \
example.mod

This is the same as Example 2 except the searching is done without preprocessing the sequences into suffix trees.