Figure 13.

Dimer substitution matrix. This matrix specifies the contribution to the total gap penalty for a pair of sequences for each possible pair of aligned dimers. Here, g is the per-gap penalty, e is the gap-extension penalty. The problem case -X ↔ -- is approximated as tg, where t is a tunable parameter.

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