Simulated Annealing with Previous Solutions Applied to DNA Sequence Alignment

Algorithm 3

Pseudo code of SAPS.

1: Tune initial temperature (𝑇_initial)

2: Tune final temperature (𝑇_final)

3: Setting the factor cooling

4: Setting 𝑆_current with 𝑆_original

5: Add 𝑆_original to 𝑆𝑆_betters and to 𝑆_better

6: Calculate similarity of 𝑆_current

7: 𝑇 = 𝑇_initial

8: Setting 𝐿_cm

9: While (𝑇 > 𝑇_final) do

10:  𝑛 = 1

11:  While (𝐿_cm > 𝑛)

12:    Create 𝑆_new adding or removing gap to 𝑆_current

13:    Calculate similarity of 𝑆_new

14:    Obtain difference of similarity between 𝑆_new and 𝑆_current

15:    If (difference ⇐ 0) then

16:     𝑆_current = 𝑆_new

17:     If similarity (𝑆_new) > similarity (𝑆_better) then

18:      𝑆_better = 𝑆_current

19:      Add S _better to SS _betters

20:     end if

21:    else

22:     Boltzmann probability = exp(-difference/𝑇)

23:     If (Boltzmann probability) > random(0,1) then

24:      S _current = S _new

25:     end if

26:    end if

27:    𝑛 = 𝑛 + 1

28:   end while

29:   Descrease 𝑇

30:   Increase 𝐿_cm

31:   Randomly Choose S _current of SS _betters, S _better o S _original

32: end while