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CHAPTER 18. SEQUENCE ALIGNMENT
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Figure 18.13: Creating a pairwise comparison table.
18.5.2
Pairwise comparison parameters
There are four kinds of comparison that can be made between the sequences in the alignment,
as shown in figure 18.14.
Figure 18.14: Adjusting parameters for pairwise comparison.
• Gaps Calculates the number of alignment positions where one sequence has a gap and the
other does not.
• Identities Calculates the number of identical alignment positions to overlapping alignment
positions between the two sequences.
• Differences Calculates the number of alignment positions where one sequence is different
from the other. This includes gap differences as in the Gaps comparison.
• Distance Calculates the Jukes-Cantor distance between the two sequences. This number
is given as the Jukes-Cantor correction of the proportion between identical and overlapping
alignment positions between the two sequences.
• Percent identity Calculates the percentage of identical residues in alignment positions to
overlapping alignment positions between the two sequences.