# Detour: Scoring Multiple Alignments

Explore a few more practical approaches for scoring alignments.

## We'll cover the following

## 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:

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

where the sum is taken over all symbols *x* present in the column, and
$p_x$ is the frequency of symbol *x* in the column.

Previously, we saw that more highly conserved columns will have lower entropy
scores. Because we wish to maximize the alignment score, we use the negative of
entropy in order to ensure that more highly conserved columns receive higher scores.
Finding a longest path in the *t*-dimensional alignment graph therefore corresponds to
finding a multiple alignment with minimal entropy.

## SP-score

Another popular scoring approach is the **Sum-of-Pairs score (SP-score)**. A multiple
alignment *Alignment* of *t* sequences induces a pairwise alignment between the *i*-th and
*j*-th sequences, having score *s(Alignment, i, j)*. The SP-score for a multiple alignment
simply adds the scores of each induced pairwise alignment:

$Sp-Score(Alignment) = \sum_{1\leq i\leq j\leq t}^{} s(Alignment, i, j)$

`Exercise Break:`

Compute the entropy score and SP-score of Marahiel’s 3-way alignment, reproduced below.

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