Figure 6.16 presents the comparison of two hypothetical genes v and w of
the same length with a conserved domain present at the beginning of v and
at the end of w. For simplicity, we will assume that the conserved domains
in these two genes are identical and cover one third of the entire length, n, of
these genes. In this case, the path fromsource to sink capturing the similarity
between the homeodomains will include approximately 2
3n horizontal edges,
1
3n diagonalmatch edges (corresponding to homeodomains), and 2
3n vertical
edges. Therefore, the score of this path is