Dynamic Programing
Dynamic Programing Dynamic Programing
Classes of Pairwise Alignment: I. Global Alignment Best match in the entire sequences A T A C A G C G G T C T A - - C A G - G G T - T II. Local Alignment Best subsequence match A T A C A G C G G T - C T - - A C A G - G G T T - - III. Semi-Global Alignment "Glocal" Alignment
Classes of Pairwise Alignment: I. Global Alignment Best match in the entire sequences A T A C A G C G G T C T A - - C A G - G G T - T II. Local Alignment Best subsequence match A T A C A G C G G T - C T - - A C A G - G G T T - - III. Semi-Global Alignment "Glocal" Alignment Best match without penalizing gaps on the ends of the alignment T C T G T - A C C G T G - - - - - G T T A C C A T G C C
- 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 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 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
- 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
Classes of Pairwise Alignment:<br />
I. Global Alignment<br />
Best match in the entire sequences<br />
A T A C A G C G G T C T<br />
A - - C A G - G G T - T<br />
II. Local Alignment<br />
Best subsequence match<br />
A T A C A G C G G T - C T<br />
- - A C A G - G G T T - -<br />
III. Semi-Global Alignment<br />
"Glocal" Alignment<br />
Best match without penalizing gaps on the<br />
ends of the alignment<br />
T C T G T - A C C G T G - -<br />
- - - G T T A C C A T G C C
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