Sequence alignment of YPKIEAIY and MPKIIEAIYEN. An example of computing the local alignment between two sequences PAWHEAE and HEAGAWGHEE using the Smith-Waterman algorithm with the BLOSUM 50 scoring matrix. The highest score in the matrix (+28) is the optimal score for the alignment. The trace-back procedure, shown in form of arrows, shows that the optimal local alignment is AW-HE and AWGHE.
Wirawan et al. BMC Bioinformatics 2008 9:377 doi:10.1186/1471-2105-9-377