Pairwise sequence alignment

Perform a pairwise sequence alignment for the following analogous proteins ... 

Pairwise sequence alignments are typically evaluated through their constituent residue pairs. In this approach, each individual pair of residues is assigned a score, and the PSA is evaluated by summing the scores of all pairs (Figure 6.5). Because each position in the PSA is considered separately, every occurrence of the residue pair (a, b) receives the same score. Thus, for each possible (a, b) only one score... 

Profile threading methods As described in Section 6.2, algorithms that optimize threading profiles are the same as for pairwise sequence alignment and are based on dynamic programming. These methods have been introduced by Eisenberg et al. [136, 193, 194]. 

Improving Pairwise Sequence Alignment between Distantly Related Proteins... 

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