DemoA12 - Sheet1 Page 1 Demonstration: Dynamic Programming...

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Unformatted text preview: Sheet1 Page 1 Demonstration: Dynamic Programming with Similarity Matrix and Constant Gap Penalty Author: R.F. Murphy, Feb. 27, 2005 This demonstration illustrates the three steps of the basic dynamic programming method, incorporating a similarity matrix for the initialization step and a constant gap penalty. See Lecture Notes for details on the method. Suggestions: Change the sequences in cells B10 and B11 and observe how the alignment adjusts. Change the gap penalty also. For the sequences provided, note changes in alignment for penalties of 1 and 3. The sequences are entered here: 1: acdcdefg 2: acdefghi Step 1: Initialize the matrix with similarity values. a c d c d e f g a 2 -2 0 -2 0 -4 1 (this section refers to the PAM250 matrix c-2 12 -5 12 -5 -5 -4 -3 found at the bottom of this spreadsheet) d 0 -5 4 -5 4 3 -6 1 e 0 -5 3 -5 3 4 -5 f-4 -4 -6 -4 -6 -5 9 -5 g 1 -3 1 -3 1 0 -5 5 h...
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