Outline Recursion and dynamic programming Applied dynamic programming: global alignments: Needleman-Wunsch Applied dynamic programming: local alignments Smith -Waterman Substitution matrices PAM. blosUM, Gonnet Gaps- linear and affine · Alignment statistics What you need to know to optimize an alignmentOutline • Recursion and dynamic programming • Applied dynamic programming: global alignments: Needleman-Wunsch • Applied dynamic programming: local alignments – Smith-Waterman • Substitution matrices: PAM, BLOSUM, Gonnet • Gaps - linear and affine • Alignment statistics • What you need to know to optimize an alignment