Detour: Scoring Multiple Alignments

Entropy of a column

The choice of scoring function can drastically affect the quality of a multiple alignment. In the main lesson, we described a way to score t-way alignments by using a t-dimensional scoring matrix. Below, we describe more practical approaches to scoring alignments.

The columns of a t-way alignment describe a path in a t-dimensional alignment graph whose edge weights are defined by the scoring function. Using the statistically motivated entropy score, the score of a multiple alignment is defined as the sum of the entropies of its columns. Recall from Chapter 2 that the entropy of a column is equal to:

$$- \sum p_{x} \cdot log_{2}(p_{x}),$$ ...