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i am a student and i wanted to search a gene for a binding motif. I created a PWM and found several matches. My problem is i dont know how to assign P values to those scores? I've read several papers that suggest the best to create a histogram from PWM scores from random sequences and use them to create a P value. Alternatively some papers suggest that you can evaluate prediction accuracy using a gold standard set of known sites, and define the false detection rate for each score threshold.

I'm not familiar with R and i'm getting pretty lost. I've started playing with some code but again its not something i understand that well.

I imagine that this isnt very complicated and is done often. There must be a relatively simple way of doing it. Any help or direction would be appreciated beyond measure.

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