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A T C
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A T C 1 First Place a 1 at every match
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A T C 1
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INDEL -INSERTION OR DELETION (CANNOT TELL WHICH HAPPENED)
1 INDEL -INSERTION OR DELETION (CANNOT TELL WHICH HAPPENED)
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SCORING ALIGNMENT
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Scoring Alignment Cumulative Score
Allows to trace back the best alignment Do this by summing the scores as you go n,j n+1,j+1 n+1,j+2 n+2,j+1 START HERE
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Scoring Alignment Cumulative Score
Allows to trace back the best alignment Do this by summing the scores as you go n,j n+1,j+1 n+1,j+2 n+2,j+1 START HERE
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Scoring Alignment Cumulative Score
Score entered in position n, j will be Sn,j + Max score of j [n+1,j+1 OR n+1,j+2 OR n+2,j+1] n,j n+1,j+1 n+1,j+2 n+2,j+1 n
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Scoring Alignment Cumulative Score Score will be
Sn,j + Max score of j [n+1,j+1 OR n+1,j+2 OR n+2,j+1] n,j n+1,j+1 n+1,j+2 n+2,j+1 n If more sequences aligned cumulative score is derived from continued row or column.
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Score value at position n,j
The value entered at position is the sum of the value assigned for the match or mismatch at that position and the score derived from the best possible previous alignment. n,j n+1,j+1 n+1,j+2 n+2,j+1
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A T C 1
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A T C 1 O FILL OUTER ALIGNMENTS
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A T C 1
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A T C 1 START TO FILL IN CUMULATIVE SCORES
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A T C 1 A T
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A T C 1 A T +
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A T C 1
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A T C 1 A
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A T C 1 A
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A T C 1 A T +
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A T C 1 2 A T +
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A T C 1 1* 2
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A T C 1 1* 2 WHY A 1?
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ADDING MAXIMUM VALUE FOR CUMULATIVE SCORE
1 1* 2 ADDING MAXIMUM VALUE FOR CUMULATIVE SCORE
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ADDING MAXIMUM VALUE FOR CUMULATIVE SCORE
1 1* 2 ADDING MAXIMUM VALUE FOR CUMULATIVE SCORE
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ADDING MAXIMUM VALUE FOR CUMULATIVE SCORE
1 1* 2 CATC A.T ATC A.T ADDING MAXIMUM VALUE FOR CUMULATIVE SCORE
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ADDING MAXIMUM VALUE FOR CUMULATIVE SCORE
1 1* 2 INSERTING A GAP GIVES ALIGNMENT SCORE OF 1 CATC A.T ADDING MAXIMUM VALUE FOR CUMULATIVE SCORE
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A T C 1 2
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A T C 1 2
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A T C 1 0+1 2
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A T C 1 2
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A T C 1 2
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A T C 1 2 +
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A T C 1 2 +
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A T C 1 2
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A T C 1 2
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A T C 1 2
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A T C 1 2
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A T C 1 2
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A T C 1 2
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A T C 1 1+2 2
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A T C 1 3 2
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A T C 1 3 2
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A T C 1 3 2
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A T C 1 0+2 3 2
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What does this value mean in terms of an alignment?
C 1 2 3 What does this value mean in terms of an alignment?
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A T C 1 2 3 T C START BY ALIGNING THESE RESIDUES
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A T C 1 2 3 T C A C * A Inserting a gap
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A T C 1 2 3 T C A T C * A T
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A T C 1 2 3 Two matches in this alignment, so it is scored as 2
2 3 Two matches in this alignment, so it is scored as 2 T C A T C * A T
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A T C 1 2 3
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A T C 1 2 3
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A T C 1 2 3
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A T C 1 2 3
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A T C 1 2 3 +
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A T C 1 2 3
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A T C 1 2 3
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A T C 1 2 3 Only add a single maximum value
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A T C 1 2 3
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A T C 1 2 3 +
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A T C 1 2 3
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A T C 1 2 3
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A T C 1 2 3
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A T C 1 2 3
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A T C 1 4 2 3
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A T C 1 4 2 3
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A T C 1 4 2 3
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A T C 1 0+3 4 2 3
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A T C 1 3 4 2
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A T C 1 3 4 2
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A T C 1 3 4 2
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A T C 1 3 4 2
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A T C 1 3 4 2
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A T C 1 3 4 2
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A T C 1 3 4 2
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A T C 1 3 4 2
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A T C 1 3 4 2
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A T C 1 0+2 3 4 2
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A T C 1 2 3 4
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A T C 1 2 3 4
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A T C 1 2 3 4
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A T C 1 0+3 2 3 4
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A T C 1 3 2 4
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A T C 1 3 2 4
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A T C 1 3 2 4
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A T C 1+4 3 2 1 4
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A T C 5 3 2 1 4
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A T C 5* 3 2 1 4 Trace Back -start with maximum score
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A A A T C 5* 3 2 1 4 Trace Back -start with maximum score
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A A A T C 5* 3 2 1 4 Next highest in diagonal
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A T A T A T C 5* 3 2 1 4 Next highest in diagonal
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A T C A T C A T C A T * A T C 5* 3 2 1 4 COMPLETE ALIGNMENT
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A G T C 7 5 4 3 2 1 6
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A G T C 7 5 4 3 2 1 6 * A A
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A G T C 7 5 4 3 2 1 6 A G A G
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A G T C 7 5 4 3 2 1 6 A G T A G C
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A G T C 7 5 4 3 2 1 6 A G T C A G * C 4 gives higher score than 5
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A G T C 7 5 4 3 2 1 6 A G T C A A G * C A
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A G T C 7 5 4 3 2 1 6 A G T C A T A G * C A T
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A G T C 7 5 4 3 2 1 6 A G T C A T G A G * C A T G
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A G T C 7 5 4 3 2 1 6 A G T C A T G G A G * C A T G C
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A G T C 7 5 4 3 2 1 6 A G T C A T G G C A G * C A T G C C
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A G T C 7 5 4 3 2 1 6 A G T C A T G G C * A G * C A T G C C T
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A G T C 7 5 4 3 2 1 6 A G T C A T G A G * C A T G HERE YOU HAVE EQUIVALENT CHOICES
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A G T C 7 5 4 3 2 1 6 A G T C A T G A G * C A T G NOTICE THAT NEXT MOVE CAN EITHER GO HERE
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A G T C 7 5 4 3 2 1 6 A G T C A T G A G * C A T G NOTICE THAT NEXT MOVE CAN EITHER GO HERE OR HERE
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A G T C 7 5 4 3 2 1 6 A G T C A T G G C * * A G * C A T G * C C T
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mismatch First alignment A G T C A T G G C * A G * C A T G C C T Second alignment A G T C A T G G C * * A G * C A T G * C C T gap
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mismatch First alignment A G T C A T G G C * A G * C A T G C C T Second alignment A G T C A T G G C * * A G * C A T G * C C T gap Address these issues by introducing a gap penalty
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