This webpage contains the program Motif Search accompanying the paper
Robert Osada, Elena Zaslavsky and Mona Singh. Comparative analysis of methods for representing and searching for transcription factor binding sites. Bioinformatics 2004; 20(18):3516-3525. Bioinformatics
Motif Search allows you to specify several different criteria when searching for sites, such as a p-value or an approximate false-positive rate given a set of negative examples. Motif Search is free and is licensed under the GNU General Public License (GPL); see the official GNU website for more information.
You may use the online web form, install Motif Search from source, or download one of the prebuilt binaries.
Please email questions or comments to msingh at cs.princeton.edu