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
10th Edition
ISBN:9780470458365
Author:Erwin Kreyszig
Publisher:Erwin Kreyszig
Chapter2: Second-order Linear Odes
Section: Chapter Questions
Problem 1RQ
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Question
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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