Pairwise comparison parameters
There are five kinds of
comparison that can be made between the sequences in the alignment,
as shown in figure 3.11.
Figure 3.11: 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.