International Scholarly Research Notices

Research Article

Simulated Annealing with Previous Solutions Applied to DNA Sequence Alignment

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: S_current = 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