HOMER offers solid tools and methods for interpreting ChIP-Seq experiments. In addition to UCSC visualization support and peak finding [and motif finding of course], HOMER can help assemble data across multiple experiments and look at positional specific relationships between sequencing tags, motifs, and other features. You do not need to use the peak finding methods in this package to use motif finding. (Use the bed2pos.pl program to create peak files from BED files).
Prebuilt Homer data can be found in /usr/local/apps/homer/data. If you don't see what you need, please contact us at firstname.lastname@example.org
To run homer:
$ module load homer $ cd /data/$USER/homer1 $ findMotifs.pl genelist.txt mouse motifResults/ -len 10