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kchu25 committed Aug 21, 2024
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Expand Up @@ -31,7 +31,7 @@ The function `logoplot(pfm)` produces a plot where:
# Note

### Definition of Information Content in Position Weight Matrices (PWM)
In a position weight matrix (PWM), the <b>information content</b> $IC(\cdot)$ (i.e. the "letter height") of the $i$-th column $c_i$ in a position weight matrix (PWM) is
In a position weight matrix (PWM), the "letter height", or more formally, the <b>information content</b> $IC(\cdot)$ 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 \frac{f_{\alpha i}}{\beta_\alpha}
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