alignment

# Edit distance example edit distance example contd

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Unformatted text preview: ATCCAT ATCCGAT (delete last T) (delete last A) (insert A at front) (substitute C for 3rd G) (insert G before last A) (Done) Note: Edit distance IS a distance What properties does a distance function need to satisfy? Edit Distance: Example Edit Distance: Example (cont’d) TGCATAT ATCCGAT in 5 steps TGCATAT ATCCGAT in 4 steps TGCATAT (delete last T) TGCATA (delete last A) TGCAT (insert A at front) ATGCAT (substitute C for 3rd G) ATCCAT (insert G before last A) ATCCGAT (Done) What is the edit distance? 5? TGCATAT (insert A at front) ATGCATAT (delete 6th T) ATGCATA (substitute G for 5th A) ATGCGTA (substitute C for 3rd G) ATCCGAT (Done) Alignment as a Path in the Edit Graph 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 Alignment as a Path in the Edit Graph 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) and represent indels in v and w w ith score 0. represent matches w ith score 1. The score of the alignment is 5. 9 Alignment as a Path in the Edi...
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## This note was uploaded on 02/10/2014 for the course CS 548 taught by Professor Asaben-hur during the Spring '12 term at Colorado State.

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