Provides the best op1mal alignment between two

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: ne insertion and one deletion) How to find what j goes with what i such that the “score” of the alignment is op1mized? Edit Distance: Example TGCATAT ATCCGAT in 5 steps TGCATAT TGCATA TGCAT ATGCAT ATCCAT ATCCGAT (delete last T) (delete last A) (insert A at front) (subs1tute C for 3rd G) (insert G before last A) (Done) Compu1ng Edit Distance Dynamic Programming Algorithm •  Dynamic Programming is a method for solving complex problems by breaking them down into simpler subproblems. •  Provides the best (op1mal) alignment between two sequences. •  Includes matches, mismatches, and gaps to maximize the number of matched characters. •  Score: match, mismatch, gap (affine vs. non ­ affine) Dynamic Programming Visualized 01 A A 01 2 T T 2 2 _ C 3 3 G G 4 4 T T 5 5 T _ 5 6 A A 6 7 T _ 6 7 _ C 7 Corresponding path (0,0), (1,1), (2,2), (2,3), (3,4), (4,5), (5,5), (6,6), (7,6), (7,7) Dynamic Programming...
View Full Document

This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

Ask a homework question - tutors are online