Global Sequence Alignment: the Needleman-âWunsch Algorithm

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Needleman-‐Wunsch Example M(i,j) s 1 A! S! L! V! N! D! K! s 2 0 1 2 3 4 5 6 7 0 A! 1 L! 2 V! 3 N! 4 K! 5 D! 6 K! 7
Start with base condiLons D(i,j) s 1 A! S! L! V! N! D! K! s 2 0 1 2 3 4 5 6 7 0 0 ? ? ? ? ? ? ? A! 1 ? L! 2 ? V! 3 ? N! 4 ? K! 5 ? D! 6 ? K! 7 ? What is D(1, 0), the score of the opLmal alignment of s 1 [1..1] with a gap?
Page 1 and 2: Global Sequence Alignment: the
Page 3 and 4: What is the intuiLon behind s
Page 5 and 6: Why align sequences? • Alignme
Page 7 and 8: Why align sequences? Alignments
Page 9 and 10: There are many possible alignme
Page 11 and 12: Which is the best alignment? s
Page 13 and 14: Idea: How can we find an opLm
Page 15 and 16: So what can we do?
Page 17 and 18: Some NotaLon • s 1 [1..i] = t
Page 19 and 20: The Key Insight • Think about
Page 21: Dynamic Programming Approach •
Page 25 and 26: Now compute M(i,j) row by row.
Page 27 and 28: Now compute M(i,j) row by row.
Page 29 and 30: How do we construct an opLmal
Page 31 and 32: Is this algorithm feasible? •
Page 33 and 34: When would you want a local a

Global Sequence Alignment: the Needleman-âWunsch Algorithm

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Global Sequence Alignment: the Needleman-âWunsch Algorithm