Figure 1.

Example alignment pair. Numbers identify the residues in the sequences. k1 columns – A5B-, A6B-, A7B5, and A8B6 – are found in only the left alignment. K2 columns – A7B-, A8B-, A5B5, and A6B6 – are found in only the right alignment. K3 columns – A1B1, A2B2, A3B3, and A4B4 – are found in both alignments. Alignment identity is I = (2K3)/(2K3 + K1 + K2) = (2 × 4)/(2 × 4 + 4 + 4) = 1/2.

Cartwright BMC Bioinformatics 2006 7:527   doi:10.1186/1471-2105-7-527
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