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

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Sheet1 Page 1 Demonstration: Dynamic Programming with Similarity Matrix and Constant Gap Penalty Author: R.F. Murphy, Feb. 27, 2005, Revised January 25, 2007 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...
View Full Document

This note was uploaded on 03/04/2012 for the course BIO 510 taught by Professor Miller during the Fall '06 term at Carnegie Mellon.

Ask a homework question - tutors are online