Research Article
Simulated Annealing with Previous Solutions Applied to DNA Sequence Alignment
Algorithm 3
Pseudo code of SAPS.
1: Tune initial temperature () | 2: Tune final temperature () | 3: Setting the factor cooling | 4: Setting
with | 5: Add
to
and to | 6: Calculate similarity of | 7: = | 8: Setting | 9: While ( > ) do | 10: = 1 | 11: While (
> ) | 12: Create
adding or removing gap to | 13: Calculate similarity of | 14: Obtain difference of similarity between
and | 15: If (difference 0) then | 16:
= | 17: If similarity () > similarity () then | 18:
= | 19: Add S better to SS betters | 20: end if | 21: else | 22: Boltzmann probability = exp(-difference/) | 23: If (Boltzmann probability) > random(0,1) then | 24: S current = S new | 25: end if | 26: end if | 27: = + 1 | 28: end while | 29: Descrease | 30: Increase | 31: Randomly Choose S current of SS betters, S better o S original | 32: end while |
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