The Smith-Waterman (SW) algorithm is a typical technique for local sequence 
alignment in computational biology. However, the SW algorithm does not consider 
the local behaviours of the amino acids, which may result in loss of some useful 
information. Inspired by the success of Markov Edit Distance (MED) method, this 
paper therefore proposes a novel Markov pairwise protein sequence alignment 
(MPPSA) method that takes the local context dependencies into consideration. The 
numerical results have shown its superiority to the SW for pairwise protein 
sequence comparison.