Dynamic Programing
Dynamic Programing Dynamic Programing
Needleman-Wunsch Algorithm (Cont.) Calculation Let NW(i,j) be the optimal alignment score of aligning V[1...i] and W[1...j] 0 w1 ... wj ... wm v1 : (I) +s(vi, wj) (III) +gap vi (II) +gap : vn Optimal alignment score Base case: " NW (0,0) = 0 $ # NW (0, j) = NW (0, j ! 1) + g $ % NW (i,0) = NW (i ! 1,0) + g " NW (i ! 1, j ! 1) + s(v i ,w j ) $ Recurrence: NW (i, j) = max # NW (i ! 1, j) + g $ % NW (i, j ! 1) + g For linear gap penalty model operations: match/mismatch delete insert
Dynamic Programming Approach Summary Construct an optimal alignment between two subsequences (v1v2...vi) and (w1w2...wj), (Where 0 ! i ! n and 0 ! j ! m), by considering the three cases: (I) The optimal alignment of v1,...,vi-1 with w1,...wj-1, extended by the match between vi and wj.. (II)The optimal alignment of v1,...,vi-1 with w1,...wj, extended by matching a gap character with vi. (III)The optimal alignment of v1,...,vi with w1,...wj-1, extended by matching wj with a gap character “-”. Store these optimal scores of subsequence alignments in a matrix of size (n+1) x (m+1).
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- Page 3 and 4: Importance of Sequence Alignment
- Page 5 and 6: Alignment Operation Transforming on
- Page 7 and 8: Difficulties in measuring sequence
- Page 9 and 10: Efficient way to find a best alignm
- Page 11 and 12: Problems Solvable by Dynamic Progra
- Page 13: Property of DP problems • Have ov
- Page 16 and 17: I. Global Alignment Classes of Pair
- Page 18 and 19: Classes of Pairwise Alignment: I. G
- Page 20 and 21: Classes of Pairwise Alignment: I. G
- Page 22 and 23: Global Alignment spans all the resi
- Page 24 and 25: Scoring matrix represents a specifi
- Page 26 and 27: Needleman-Wunsch Algorithm (Cont.)
- Page 30 and 31: Needleman-Wunsch Algorithm (Cont.)
- Page 32 and 33: Needleman-Wunsch Algorithm Efficien
- Page 34 and 35: Needleman-Wunsch Algorithm for any
- Page 36 and 37: Needleman-Wunsch Algorithm for any
- Page 38 and 39: Local Alignment finds the most simi
- Page 40 and 41: Smith-Waterman Algorithm (Cont.)
- Page 42 and 43: Smith-Waterman Algorithm (Cont.) v1
- Page 44 and 45: Smith-Waterman Algorithm (Cont.) Ex
- Page 46 and 47: Which alignment to use Example 1. O
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- Page 54 and 55: Which alignment to use (Cont.) Exam
- Page 56 and 57: Versatility of DP Algorithm • Mem
- Page 58 and 59: References - Gusfield D. Algorithms
Needleman-Wunsch Algorithm (Cont.)<br />
Calculation<br />
Let NW(i,j) be the optimal alignment score of aligning V[1...i] and W[1...j]<br />
0<br />
w1 ... wj ... wm<br />
v1<br />
:<br />
(I)<br />
+s(vi, wj)<br />
(III)<br />
+gap<br />
vi<br />
(II)<br />
+gap<br />
:<br />
vn<br />
Optimal<br />
alignment<br />
score<br />
Base case:<br />
" NW (0,0) = 0<br />
$<br />
# NW (0, j) = NW (0, j ! 1) + g<br />
$<br />
% NW (i,0) = NW (i ! 1,0) + g<br />
" NW (i ! 1, j ! 1) + s(v i<br />
,w j<br />
)<br />
$<br />
Recurrence: NW (i, j) = max # NW (i ! 1, j) + g<br />
$<br />
% NW (i, j ! 1) + g<br />
For linear gap penalty model<br />
operations:<br />
match/mismatch<br />
delete<br />
insert
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