The storm software is designed to scan through sequences in search of binding sites that match given motifs. The program is very flexible and provides a number of alternatives to determine matching criteria for motifs. For a full list of options, see the examples link.
A notable feature of the storm program is that it is able to assign p-values to motif matches by using information compiled from sequence databases in the form of a gk-table . We provide a number of pre-computed gk-tables through the Database files link. We also provide the software used to construct gk-tables through the download link and examples of how to use it here .
The modstorm program is an extension of the storm program to search for modules of transcription factor binding sites. All of the threshold options that are available in storm are also available in modstorm . The modstorm software allows for many different ways to search for modules. A window size that all factors must occur in can be specified, or the organization of the module can be specified. Examples of use are available here.
For details, please see the FAQ link or the reference listed below.
Dustin E Schones, Andrew D Smith and Michael Q Zhang
Statistical significance of cis-regulatory modules
BMC Bioinformatics 2007, 8:19