Dynamic Programming Example: The answer is given. Please give me a better explan
ID: 3732480 • Letter: D
Question
Dynamic Programming Example:
The answer is given. Please give me a better explanation and how to fill in the matrice completely! Much appreciated.
no time involvea; simulated annealing is just a better sampling technique. 11) We want to find the best alignment(s) between the DNA sequences AGTATCT and AGATGC. The scoring scheme S is defined as follows: S(i,j)-1 ifi-j, and S(ij)- 0 otherwise There is a constant gap penalty of -1 (penalty for the first position counts; see table below). The score Sbest and the number N of optimal alignments are (show your final dynamic programming matrix and the best possible alignment (s) for full credit) 0 A) Sbest- 3, N-2 B) Sbest-3, N-1 C) Sbest-4,N-1 E) Sbest-4; N-3Explanation / Answer
Answer :
D) SBEST = 3, N = 3.
Explanation :
In the given question, three optimal alignments are found. Optimal alignments are the best alignment between two sequences. In the alignment two things are considered mainly. They are the number of matches in the alignment and number of gaps.
When we compare two sequences, match between the bases of two sequences are given as positive score . After adding all matches between the bases in two sequences we subtract the gap score which is in this case is equal to -1 * number of gap inserted.
Best score is equal to that is the highest score after subtracting the gap score.
Please consider that gaps are not present in the sequences, we are inserting the gap in order to get the maximum matches between two sequences. Hence, optimal alignment in this question. Is the alignment that are giving best matches with minimum gaps introduced . Hence, we are getting 3 optimal alignment and score of the optimal alignment is 3.
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