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kchu25 committed Aug 21, 2024
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### Definition of Information Content in Position Weight Matrices (PWM)
In a position weight matrix (PWM), the "letter height", or more formally, the *information content* $IC(\cdot)$ of the $i$-th column $c_i$, quantifies how conserved the nucleotides are at that position compared to a background model. It is calculated using the formula:

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

where $f_{\alpha i}$ is the frequency of nucleotide $\alpha\in\Set{A,C,G,T}$ at the $i$-th column of a PWM and $\beta_\alpha$ denotes the genomic background frequency of nucleotide $\alpha$.

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