Dynamic Programing

More documents

Recommendations

Info

Alignment Operation Transforming one string into the other by a series of edit operations on individual characters Edit operations was first introduced in the edit distance concept by Levenshtein 1966. • Insertion (I) of a character into the first string • Deletion (D) of a character from the first string • Substitution (S) of a character in the first string that mismatches the aligned character in the second string • Match (M) of a character in the first strings with a character in the second string Example: V = THISLINE and W = ISALIGNED V: T H I S - L I - N E - | | | | | | Edition on V: D D M M I M M I M M I | | | | | | W: - - I S A L I G N E D
Difficulties in measuring sequence similarities • Sequences usually differ in length • Sequences may only have very small region of similarity • Some substitution are more likely than others
Page 1 and 2: Dynamic Programming and Pairwise Se
Page 3 and 4: Importance of Sequence Alignment
Page 5: Alignment Operation Transforming on
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 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 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
show all

Dynamic Programing

Create successful ePaper yourself

Delete template?

Save as template?