Cpt S 580 Fundamental Algorithms in Computational Genomics
Global Alignment: Dynamic Progamming Table
s1: acagagtaac
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s2: acaagtgatc
– a c a a g t g a t c
match=1, mismatch=-1, gap=-1
Cpt S 580: Fundamental Algorithms in Computational Genomics, Spring 2007
Global Alignment: Dynamic Progamming Table
s1: acagagtaac
s2: acaagtgatc
– a c A a g t g a t c
– 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
match=1, mismatch=-1, gap=-1
Cpt S 580: Fundamental Algorithms in Computational Genomics, Spring 2007
Global Alignment: Dynamic Progamming Table
s1: acagagtaac
s2: acaagtgatc
– a c A a g t g a t c
– 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
match=1, mismatch=-1, gap=-1
Cpt S 580: Fundamental Algorithms in Computational Genomics, Spring 2007
Global Alignment: Dynamic Progamming Table
s1: acagagtaac
s2: acaagtgatc
– a c A a g t g a t c
– 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
a -1 1 0 -1 -2 -3 -4 -5 -6 -7 -8
match=1, mismatch=-1, gap=-1
Cpt S 580: Fundamental Algorithms in Computational Genomics, Spring 2007
Global Alignment: Dynamic Progamming Table
s1: acagagtaac
s2: acaagtgatc
– a c A a g t g a t c
– 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
a -1 1 0 -1 -2 -3 -4 -5 -6 -7 -8
c -2 0 2 1 0 -1 -2 -3 -4 -5 -6
match=1, mismatch=-1, gap=-1
Cpt S 580: Fundamental Algorithms in Computational Genomics, Spring 2007
Global Alignment: Dynamic Progamming Table
s1: acagagtaac
s2: acaagtgatc
– a c A a g t g a t c
– 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
a -1 1 0 -1 -2 -3 -4 -5 -6 -7 -8
c -2 0 2 1 0 -1 -2 -3 -4 -5 -6
a -3 -1 1 3 2 1 0 -1 -2 -3 -4
g -4 -2 0 2 2 3 2 1 0 -1 -2
a -5 -3 -1 1 3 2 2 1 2 1 0
g -6 -4 -2 0 2 4 3 3 2 1 0
t -7 -5 -3 -1 1 3 5 4 3 3 2
a -8 -6 -4 -2 0 2 4 4 5 4 3
a -9 -7 -5 -3 -1 1 3 3 5 4 3
c -10 -8 -6 -4 -2 0 2 2 4 4 5
match=1, mismatch=-1, gap=-1
Cpt S 580: Fundamental Algorithms in Computational Genomics, Spring 2007
Global Alignment: Dynamic Progamming Table
s1: acagagtaac
s2: acaagtgatc
– a c A a g t g a t c
– 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
a -1 1 0 -1 -2 -3 -4 -5 -6 -7 -8
c -2 0 2 1 0 -1 -2 -3 -4 -5 -6
a -3 -1 1 3 2 1 0 -1 -2 -3 -4
g -4 -2 0 2 2 3 2 1 0 -1 -2
a -5 -3 -1 1 3 2 2 1 2 1 0
g -6 -4 -2 0 2 4 3 3 2 1 0
t -7 -5 -3 -1 1 3 5 4 3 3 2
a -8 -6 -4 -2 0 2 4 4 5 4 3
a -9 -7 -5 -3 -1 1 3 3 5 4 3
c -10 -8 -6 -4 -2 0 2 2 4 4 5
match=1, mismatch=-1, gap=-1
Cpt S 580: Fundamental Algorithms in Computational Genomics, Spring 2007
Global Alignment:
– a c a a g t g a t c
– 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10
a -1 1 0 -1 -2 -3 -4 -5 -6 -7 -8
c -2 0 2 1 0 -1 -2 -3 -4 -5 -6
a -3 -1 1 3 2 1 0 -1 -2 -3 -4
g -4 -2 0 2 2 3 2 1 0 -1 -2
a -5 -3 -1 1 3 2 2 1 2 1 0
g -6 -4 -2 0 2 4 3 3 2 1 0
t -7 -5 -3 -1 1 3 5 4 3 3 2
a -8 -6 -4 -2 0 2 4 4 5 4 3
a -9 -7 -5 -3 -1 1 3 3 5 4 3
c -10 -8 -6 -4 -2 0 2 2 4 4 5
a c a g a g t – a a c
| | | | | | | x |
a c a – a g t g a t c
Alignment (from path)
s1: acagagtaac
s2: acaagtgatc
Cpt S 580: Fundamental Algorithms in Computational Genomics, Spring 2007
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