Alignment Key
3
Alignment Key Lesson 5 and 6 CSCI 451/558 Thanks to Michael Arneson for t he all-possible alignment answers Needleman-Wunsch algorith m. Match reward of +1, a gap penalty of -1, and a zero mismatch penalty. G T A T G 0 -1 -2 -3 -4 -5 G -1 ↖1 0 -1 -2 -3 C -2 ↑0 ↖1 0 -1 -2 A -3 ↑-1 0 ↖2 1 0 T -4 -2 ↖0 1 ↖3 2 A -5 -3 -1 ↖1 ↑2 3 A -6 -4 -2 0 ↖↑1 2 G -7 -5 -3 -1 0 ↖2 What is the alignment score? 2 Draw the backtrack arrows. Show the two strings properly aligned G__TATG GTAT__G GCATAAG GCATAAG Needleman-Wunsch algorith m. Match reward of +1, a gap penalty of -1, and a zero mismatch penalty. G C C G C 0 -1 -2 -3 -4 -5 A ↑-1 0 -1 -2 -3 -4 T ↑-2 -1 0 -1 -2 -3 G -3 ↖-1 -1 0 0 -1 C -4 -2 ↖0 0 0 1 C -5 -3 -1 ↖1 0 1 A -6 -4 -2 0 ↖1 0 C -7 -5 -3 -1 0 ↖2 What is the alignment score? 2 Draw the backtrack arrows. Show the two strings properly aligned __GCCGC ATGCCAC
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Transcript of Alignment Key
8/8/2019 Alignment Key
http://slidepdf.com/reader/full/alignment-key 1/3
Alignment Key Lesson 5 and 6 CSCI 451/558
Thanks to Michael Arneson for the all-possible alignment answers
Needleman-Wunsch algorithm. Match reward of +1, a gap penalty of -1, and a zero mismatch penalty.
G T A T G
0 -1 -2 -3 -4 -5
G -1 ↖1 0 -1 -2 -3
C -2 ↑0 ↖1 0 -1 -2
A -3 ↑-1 0 ↖2 1 0
T -4 -2 ↖0 1 ↖3 2
A -5 -3 -1 ↖1 ↑2 3
A -6 -4 -2 0 ↖↑1 2
G -7 -5 -3 -1 0 ↖2
What is the alignment score?
2
Draw the backtrack arrows.
Show the two strings properly aligned
G__TATG GTAT__G
GCATAAG GCATAAG
Needleman-Wunsch algorithm. Match reward of +1, a gap penalty of -1, and a zero mismatch penalty.
G C C G C
0 -1 -2 -3 -4 -5
A ↑-1 0 -1 -2 -3 -4
T ↑-2 -1 0 -1 -2 -3
G -3 ↖-1 -1 0 0 -1
C -4 -2 ↖0 0 0 1
C -5 -3 -1 ↖1 0 1
A -6 -4 -2 0 ↖1 0
C -7 -5 -3 -1 0 ↖2
What is the alignment score?
2
Draw the backtrack arrows.
Show the two strings properly aligned
__GCCGC
ATGCCAC
8/8/2019 Alignment Key
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Alignment Key Lesson 5 and 6 CSCI 451/558
Needleman-Wunsch algorithm. Match reward of +1, a gap penalty of -1, and a zero mismatch penalty.
G A T T A C A
0 -1 -2 -3 -4 -5 -6 -7
G -1 ↖1 0 -1 -2 -3 -4 -5
A -2 ↑0 ↖2 1 0 -1 -2 -3A -3 -1 ↖↑1 ↖2 1 1 0 -1
C -4 -2 ↑0 ↖↑1 2 1 2 1
C -5 -3 -1 ↖↑0 1 2 2 2
T -6 -4 -2 0 ↖1 1 2 2
A -7 -5 -3 -1 0 ↖2 1 3
G -8 -6 -4 -2 -1 1 ↖2 2
A -9 -7 -5 -3 -2 0 1 ↖3
What is the alignment score?
3
Draw the backtrack arrows.
Show the two strings properly aligned
GAT__TACA G_A_TTACA GA__TTACA G_AT_TACA
GAACCTAGA GAACCTAGA GAACCTAGA GAACCTAGA
Smith-Waterman algorithm. Match reward of +1, a gap penalty of -1, and a mismatch penalty of -1.
G C G C C G A T T A C A C C G C
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0
A 0 0 0 0 0 0 0 2 1 0 1 0 1 0 0 0 0
A 0 0 0 0 0 0 0 1 1 0 1 0 ↖1 0 0 0 0
C 0 0 1 0 1 1 0 0 0 0 0 2 1 ↖2 1 0 1
C 0 0 1 0 1 2 1 0 0 0 0 1 1 2 ↖3 2 1
T 0 0 0 0 0 1 1 0 1 1 0 0 0 1 2 2 1
A 0 0 0 0 0 0 0 2 1 0 2 1 1 0 1 1 1
G 0 1 0 1 0 0 1 1 1 0 1 1 0 0 0 2 1
A 0 0 0 0 0 0 0 2 1 0 1 0 2 1 0 1 1
What is the alignment score?
3
Draw the backtrack arrows.
Show the two strings properly aligned
GCGCCGATTACACCGC
GAACCTAGA
8/8/2019 Alignment Key
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Alignment Key Lesson 5 and 6 CSCI 451/558
1. Complete the following matrix for aligning the two given sequences using the Smith-Waterman algorithm. Assume a
match reward of +1, a gap penalty of -1, and a mismatch penalty of -1.
A C C G G C G G C A T G T A G A
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 1 1 0 0 ↖1 0 0 1 0 0 0 0 0 0 0
G 0 0 0 0 2 1 0 ↖2 1 0 0 0 1 0 0 1 0G 0 0 0 0 1 3 2 1 ↖3 2 1 0 1 0 0 1 0
A 0 1 0 0 0 2 2 1 ↑2 2 3 2 1 0 1 0 2
C 0 0 2 1 0 1 3 2 1 ↖3 2 2 1 0 0 0 1
A 0 1 1 0 0 0 2 2 1 2 ↖4 3 2 1 1 0 1
What is the alignment score?
4
Draw the backtrack arrows.
Show the two strings properly aligned
ACCGGCGG_CATGTAGA
CGGACA
