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Topics - mora

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General Discussion / IC from PSAM
« on: May 24, 2019, 04:36:26 pm »
What does the information content (IC) from logos built from a PSAM matrix mean? how does this differ from IC inferred from a classic PSSM/PWM matrix?

Also, is there any information about how LogoGenerator calculate the IC in bits from the values in the PSAM? I assume it has to be very different from how it is calculated according to classic PWM right? (see link)
https://en.wikipedia.org/wiki/Position_weight_matrix

 

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General Discussion / How do I choose the topology -topo in MatrixREDUCE or MotifREDUCE?
« on: September 13, 2018, 04:23:27 pm »
Is topology equal to kmers size of the binding site? what if I want to explore kmer sizes > 8?

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