Global Sequence Alignment: the Needleman-âWunsch Algorithm

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Which sequence is more “similar” to s 1 ? s 1 = ASLVNDK! s 2 = ALVNKDK OR s 3 = AFPSTW!
What is <strong>the</strong> intuiLon behind s 2 seeming more similar? We can write s1 and s2 in a way that juxtaposes more idenLcal characters than s1 and s3: s 1 = ASLVN-DK! s 2 = A-LVNKDK! s 2 = A LVN DK s 1 = ASLVNDK! s 3 = AFPSTW-! s 3 = A These juxtaposiLons are called alignments.
Page 1: Global Sequence Alignment: the
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 and 22: Dynamic Programming Approach •
Page 23 and 24: Start with base condiLons D(i,j
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

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Global Sequence Alignment: the Needleman-âWunsch Algorithm