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Dynamic programming for sequence and structure comparison and searching

In this section, the basic dynamic programming method for sequence alignment is described [Šali & Blundell, 1990]. This method forms the core of the pairwise and multiple sequence and structure comparisons as well as of the sequence database searching.

Subsections

- Pairwise comparison
- Variable gap penalty
- Local versus global alignment
- Similarity versus distance scores
- Multiple comparisons