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Wunsch Global Alignment (Scoring System: Match 2, Mismat e first row and column with gap initialization conditions. e match or mis-match score in the upper left corner of each cell ( e 3 values that correspond to the 3 adjacent cells' score along the : Left cell, Diagonal cell, and Upper cell (e.g., -4 2 -4). e final score F(ij) of each cell as the maximum of the 3 choices f he possible directions from each cell as 1 or more arrows. possible, optimal, global alignment paths through the grid with a t corner of each valid cell. t all possible global, optimal alignments. Example:

Wunsch Global Alignment (Scoring System: Match 2, Mismat e first row and column with gap initialization conditions. e match or mis-match score in the upper left corner of each cell ( e 3 values that correspond to the 3 adjacent cells' score along the : Left cell, Diagonal cell, and Upper cell (e.g., -4 2 -4). e final score F(ij) of each cell as the maximum of the 3 choices f he possible directions from each cell as 1 or more arrows. possible, optimal, global alignment paths through the grid with a t corner of each valid cell. t all possible global, optimal alignments. Example:

Advanced Engineering Mathematics
Advanced Engineering Mathematics
10th Edition
ISBN:9780470458365
Author:Erwin Kreyszig
Publisher:Erwin Kreyszig
Chapter2: Second-order Linear Odes
Section: Chapter Questions
Problem 1RQ
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Fill in the grids below for A) a Needleman-Wunsch global alignment and then B) a Smith-Waterman local alignment. See the 04-AlignmentsAndTrees PDF for help with the algorithm. Submit a scan of both part A and part B as a PDFS. A) Needleman-Wunsch Global Alignment (Scoring System: Match 2, Mismatch -1, and Gap -2) 1) Fill in the first row and column with gap initialization conditions. 2) Fill in the match or mis-match score in the upper left corner of each cell (e.g., 2 below). 3) Fill in the 3 values that correspond to the 3 adjacent cells' score along the bottom of each cell in the order: Left cell, Diagonal cell, and Upper cell (e.g., -4 2 -4). 4) Fill in the final score F(ij) of each cell as the maximum of the 3 choices from part 3. 5) Specify the possible directions from each cell as 1 or more arrows. 6) Mark all possible, optimal, global alignment paths through the grid with a filled in circle in the upper left corner of each valid cell. 7) Write out all possible global, optimal alignments. Example: ΑΑΤAC || AA-GC A T с C Match: 2 mismatch: 2 3 4 5 Gap: -2 -2 2 -4 2 -4 A 1 -2 T 2 C 3 G 4 Show optimal alignment strings (hint – there are two):
Transcribed Image Text:Fill in the grids below for A) a Needleman-Wunsch global alignment and then B) a Smith-Waterman local alignment. See the 04-AlignmentsAndTrees PDF for help with the algorithm. Submit a scan of both part A and part B as a PDFS. A) Needleman-Wunsch Global Alignment (Scoring System: Match 2, Mismatch -1, and Gap -2) 1) Fill in the first row and column with gap initialization conditions. 2) Fill in the match or mis-match score in the upper left corner of each cell (e.g., 2 below). 3) Fill in the 3 values that correspond to the 3 adjacent cells' score along the bottom of each cell in the order: Left cell, Diagonal cell, and Upper cell (e.g., -4 2 -4). 4) Fill in the final score F(ij) of each cell as the maximum of the 3 choices from part 3. 5) Specify the possible directions from each cell as 1 or more arrows. 6) Mark all possible, optimal, global alignment paths through the grid with a filled in circle in the upper left corner of each valid cell. 7) Write out all possible global, optimal alignments. Example: ΑΑΤAC || AA-GC A T с C Match: 2 mismatch: 2 3 4 5 Gap: -2 -2 2 -4 2 -4 A 1 -2 T 2 C 3 G 4 Show optimal alignment strings (hint – there are two):
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