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kchu25 committed Aug 21, 2024
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# Note

### Default genomic background
The information content $IC(\cdot)$ (i.e. the "letter height") of the $i$-th column $c_i$ in a position weight matrix (PWM) is

$$
IC(c_i) = \sum_{\alpha}\,f_{\alpha i}\,\log_2 \frac{f_{\alpha i}}{\beta_\alpha}
IC(c_i) = \sum_{\alpha}f_{\alpha i}\log_2 \frac{f_{\alpha i}}{\beta_\alpha}
$$

where $f_{\alpha i}$ the frequency of nucleotide $\alpha\in {A,C,G,T}$ at the $i$-th column of a PWM. The $4$-dimensional vector $\beta$ is the assumed genomic background
where $f_{\alpha i}$ the frequency of nucleotide $\alpha\in\Set{A,C,G,T}$ at the $i$-th column of a PWM. The $4$-dimensional vector $\beta$ is the assumed genomic background

By default, the background $\beta$ is assumed to be flat, i.e. $\beta=(0.25, 0.25,0.25,0.25)$.

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