GA for Sequence Alignment

1
GA for Sequence Alignment

• Pair-wise alignment
• Multiple string alignment

2
Pairwise Sequence Alignment

• VNRLQQNIVSLEVDHKVANYKP
• VNRLQQSIVSLRDAFNDGELD HRVLNYKP
• Solving by a dynamic programming using Dayhoff
  matrics
• Each pairwise alignment needs O(n1n2)
• VNRLQQNIVSL__________EVDHKVANYKP
• VNRLQQSIVSLRDAFND GELD HRVLNYKP

3
How to implement a GA ?

• Representation
• Fitness
• Operators design
• Selection strategy

4
Pair-wise Alignment Representation

• How do you think?
• For example (my intuitively way)
• Guess a length n
• Chromosome

5
Pair-wise Alignment Representation

• So the chromosome becomes
• You can also use the gap position

(1,2,4,5,6,8.)
(2,4,5,7,8,10.)
6
Pair-wise Alignment Fitness Function

• Simplest
• Match 1
• Dismatch -2
• Gap -1
• Using the scoring matrix
• Protein PAM,
• DNA substitution matrix
• Summarize the total score.

7
Pair-wise Alignment Genetic Operators

• All our previous operators.
• Image one!!!
• Selection
• Try it!!!

8
Conclusion About Pair-wise Alignment

• DP can solve it in O(NM)
• GA cant have too much advantage.

9
RPCVCPVLRQAAQ s1 RPCVC_
P__VLRQAAQ a1 RPCACCPVLRQVVQ s2
RPCACCP__VLRQVVQ a2 KPCLCPRQLRQV
s3 KPCLC_ P RQLRQV_ _ a3 KPCCPRQAAQ
s4 KPC_C_ P____ RQAAQ a4 S A
10
Multiple String Alignment Representation

• How do you think?
• For example (my intuitively way)
• Guess a length n
• Chromosome

11
Multiple String Alignment Representation

• So the chromosome becomes
• You can also use the gap position
• Need fewer space
• Some good operators..

(1,2,4,5,6,8.)
(2,4,5,7,8,10.)

12
Multiple String Alignment Fitness Function

• The most hard part
• You can never know what is the real scoring
  system! Even biologists!!!
• Approximation
• Using SOP (sum of pairs)
• The most widely used
• Using PAM,
• Motif-based