Figure 1.

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[13]. 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
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