Can someone explain to me how the numbers (in red) are filled in And how they co

Question

Can someone explain to me how the numbers (in red) are filled in And how they come to the conclusion? Thanks!

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(i.j) 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 0 0 A) Sbest 3, N-2 B) Sbest-3, N 1 C) Sbest-4, N-1 D) Sbest-3, N 3 E) Sbest-4; N-3

Explanation / Answer

This is basically a dynamic programming method which is used to find the best possible way to allign the sequences.

here the gap penality is -1 match will be given 1 and mismatch is -1.

so in the first box A in the row and A in column is matching.

if row and coloumn are matching then add +1 to diagonal number and gap penality value -1 to number in upper column and -1 gap penality value to the left coloumn that is how all the boxes are filled. follow the same method till the end box.

there are the best possible alignments for the table given and those are represented by the blue , green and red arrowmarks. the scores are choosen diagonally the arrow mark from the bottom will show in the direction which will have highest number in the given diagonal ,upper and left box.it gives the best possible alignment between two sequences.

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