Research Article
Simulated Annealing with Previous Solutions Applied to DNA Sequence Alignment
Algorithm 2
Pseudo code SA applied to Sequence Alignment.
1: Tune initial temperature () | 2: Tune final temperature () | : Setting cooling factor | 4: Create
from Initial solution | 5: Calculate similarity of | 6: = | 7: Setting | 8: While ( > ) do | 9: = 1 | 10: While (
> ) | 11: Create
adding or removing gaps to | 12: Calculate similarity of | 13: Obtain difference similarity between
and | 14: If (difference 0) then | 15: Scurrent = S new | 16: If similarity () > similarity () then | :
= | : end if | 19: else | 20: Boltzmann probability = exp(−difference/) | 21: If (Boltzmann probability) > random(0,1) then | 22:
= | 23: end if | 24: end if | 25: = + 1 | 26: end while | 27: Descrease | 28: Increase | 29: end while |
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