Global Sequence Alignment: the Needleman-âWunsch Algorithm

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The Traceback M(i,j) s 1 A! S! L! V! N! D! K! s 2 0 1 2 3 4 5 6 7 0 0 0 0 0 0 0 0 0 A! 1 0 1 1 1 1 1 1 1 L! 2 0 1 1 2 2 2 2 2 V! 3 0 1 1 2 3 3 3 3 N! 4 0 1 1 2 3 4 4 4 K! 5 0 1 1 2 3 4 4 5 D! 6 0 1 1 2 3 4 5 5 K! 7 0 1 1 2 3 4 5 6 Trace the path followed to get M(n,m). Align s 1 [i] and s 2 [j]. Align gap and s 2 [j]. Align gap and s 1 [i]. There may be more than one path/opLmal alignment.
Is this algorithm feasible? • It takes roughly nm + (n + m) operaLons to fill in the table and do the traceback. • QuadraLc run Lme is much be[er than exponenLal!
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 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: How do we construct an opLmal
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