I spent some time over the last week adding fairly simple motif searching to Cartwheel, my bioinformatics site for biologists doing cis-regulatory analysis of genomic sequence. The new features include the ability to define and search with IUPAC and position-weight matrix (PWM) motifs, as well as visualization of motif search results on actual sequence.

I made a 5 minute screencast demo; take a look!

--titus