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so lets now discuss position weight matrices a more practical application of uh entropy and relative entropy towards identifying tf binding sites so now that we have some basic understanding of what entropy and relative entropy is uh its time to go back to discussing how to represent binding sites for a particular transcription factor that youve identified from for example the peak culling at the very end of the chipseq protocol and so suppose that you have a set of align binding sites of your given transcription factor theres a couple of different common ways that tfps are represented so the classic way that was first used is basically whats called the consensus sequence which is basically just a representation uh that summarizes uh the most frequently observed bases at each given position in the bonding site and so youll notice for the single uh for the consensus sequence uh representation theres a whole bunch of letters that you probably dont recognize like vdr twr so on it
