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Dynamic Programing Part A

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15 views

Dynamic Programing Part A

Uploaded by

aimalktk02
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Dynamic programing

Global Alignment- Needleman Wunch


Sequence Alignment Algorithms
• The algorithm that drives global alignment is the Needleman-Wunsch
algorithm, and the algorithm that drives local alignment is the Smith-
Waterman algorithm.
• Both these algorithms are examples of dynamic programming.
Dynamic programming is a method for solving complex problems by
breaking them down into simpler subproblems.
• In the case of sequence alignment, dynamic programming involves
setting up a two-dimensional matrix in which one sequence is listed
vertically and the other sequence is listed horizontally; then
calculating the scores, one row at a time.
Needleman-Wunsch algorithm for global
alignment
Step 1 Initialization
Step 1 Initialization
Step 1 Initialization
-2 -2 -2 -2 -2

-2

-2

-2

-2
Step 2 Matrix Filling
Step 2 Matrix Filling
Step 2 Matrix Filling
Step 3 Trace back
Important steps for writing the alignment
• To write the alignment we have to consider the arrows not the values
• we have to write the aligned sequences from left to right

4
T& T is a match so C&C is a match so
the arrow goes the arrow goes
diagonally diagonally

G&G is a match so
the arrow goes
Diagonally again
Now A&T is a
mismatch so
the arrow goes
horizontally
towards the highest
Valued neighbor

Now A&A is a
mismatch again so
the arrow goes
diagonally
Final sequence alignment

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