Pairwise comparison parameters
There are five kinds of
comparison that can be made between the sequences in the alignment,
as shown in figure 13.14.
Figure 13.14: 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. An overlapping alignment position is a position where at least one residue is present, rather than only gaps.
- 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.