Optional Parameters

-out <filename>

Option to specify the output file to write hits in oedu format.

[default = sitehopper_hits.oedu]

-max_hits <value>

Option to specify the maximum number of hits to write out. Note that if fewer than this value are found, all hits will be written out

[default = 200]

-normalize_and_rescore <bool>

Option to normalize the sitehopper score of hits by the difference in binding site size between query and hit.

[default = false]

-prefix <prefix>

Prefix used to name output files, default is blank

-log <logfile>

The argument for this flag specifies the name of the log file. This overrides any specified prefix.

[default = sitehopper_search_output.log]

-settings <settingsfile>

The argument for this flag specifies the name of the settings file. This overrides any specified prefix.

[default = sitehopper_search_settings.param]

[ Aliases = -settings ]

-verbose : Triggers copious logging output