Pairwise residue matches

Figure 6.5. Scoring pairwise alignments. Scoring schemes are comprised of a substitution matrix (S) and gap penalty. Here we consider a pairwise comparison of nucleotide sequences, and the matrix S scores +1 for a match and -1 for a mismatch (left). Three alignments of X and Y are shown, and each is scored using both a linear and an affine gap penalty. The score of each residue pair is shown beneath it, and these are summed to produce the alignment score. Note that the affine gap penalty scores neighboring gaps as -3 and -1 the ordering is not determined, but the end result is their sum -4.

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