Dynamic Programing
Dynamic Programing Dynamic Programing
Needleman-Wunsch Algorithm for any gap penalty models Does affine gap model work with simple Needleman-Wunsch Algorithm we just saw w1 ... wj ... wm v1 : vi 0 + (j) gap +(j-1)gap + (i-1) gaps +s(vi, wj) +gap +gap +(i) gaps : vn Optimal alignment score
Needleman-Wunsch Algorithm for any gap penalty models Does affine gap model work with simple Needleman-Wunsch Algorithm we just saw w1 ... wj ... wm v1 : vi 0 + (j) gap +(j-1)gap + (i-1) gaps +s(vi, wj) +gap +gap +(i) gaps : vn Optimal alignment score NW (i, j) = max # NW (i ! 1, j ! 1) + s(v i ,w j ) % $ [NW (i ! n gap , j) + w(n gap1 )] 1"ngap1 "i % &% [NW (i, j ! n gap2 ) + w(n gap2 )] 1"ngap 2 " j match/mismatch delete insert
- Page 1 and 2: Dynamic Programming and Pairwise Se
- 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 28 and 29: Needleman-Wunsch Algorithm (Cont.)
- Page 30 and 31: Needleman-Wunsch Algorithm (Cont.)
- Page 32 and 33: Needleman-Wunsch Algorithm Efficien
- 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
- Page 48 and 49: Which alignment to use Example 1. O
- Page 50 and 51: Which alignment to use Example 1. O
- Page 52 and 53: Which alignment to use example 1 co
- 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<br />
for any gap penalty models<br />
Does affine gap model work with simple Needleman-Wunsch Algorithm we just saw<br />
w1 ... wj ... wm<br />
v1<br />
:<br />
vi<br />
0<br />
+ (j) gap<br />
+(j-1)gap<br />
+ (i-1)<br />
gaps<br />
+s(vi, wj) +gap<br />
+gap<br />
+(i)<br />
gaps<br />
:<br />
vn<br />
Optimal<br />
alignment<br />
score
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