Figure 12.

Problem dimer pair. The aligned dimer pair -X ↔ -- causes a problem because its gap penalty contribution cannot be computed without additional information. Note that the first column of indels is external; after this column is discarded, different penalties may be needed, as these two examples show.

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