Storm help

[capricy]

where did you get a stand-alone copy of Patser? Could you please some sample command lines, and how did you format your input files? Thanks.

[kalidaemon]

Hi everyone
I've been running some transcription factor binding site analysis using the Storm and Motifclass utilities in the CREAD package. I got some interesting results using a functional depth cut-off and decided to run my data through again this time using a p-value cut-off as a sort of sanity check. As always with this sort of analysis, this opened a huge can of worms because there is very little agreement between results. I've got a couple questions about this that I was hoping some of you could answer:
1. I know that altering parameters in one's analysis can lead to different results. Should I be surprised/concerned that my results were so different?
2. Has anyone used Storm/Motifclass? What did you find were the best parameters for your particular data-set?
3. I've also played around with DME/Matcompare and Patser. Are there any PWM or non-PWM based transcription factor binding site analysis methods that you really like working with?