Figure 11.

Dimers in the {X,-} alphabet. Gap penalties for the sequence pair (s, u) can be computed be considering all aligned pairs of dimers in the alphabet {X,-}, where X is any amino acid and - is the usual indel symbol. Four cases are highlighted. Note that an aligned pair of identical dimers never contribute a gap penalty as any indels in the dimers are necessarily external, as in the left-most example.

Edgar BMC Bioinformatics 2004 5:113   doi:10.1186/1471-2105-5-113
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