DIAlign
Initialization

Initialization

We initialize M, A and B matrices for overlap alignment and non-overlap alignment.

  • Aligning Ai with B0 without a gap. Not possible, hence, First column of M is initialized with - \(\infty\).
  • Aligning A0 with Bj without a gap. Not possible, hence, First row of M is initialized with - \(\infty\).
  • M0,0 should have zero to begin the alignment using dynamic programming.
M 0 1 2 3 4 5
0 0 - \(\infty\) - \(\infty\) - \(\infty\) - \(\infty\) - \(\infty\)
1 - \(\infty\)
2 - \(\infty\)
3 - \(\infty\)
  • Score of the best alignment between Ai and B0 that introduces a gap in A. Not possible, hence, First column of B is initialized with - \(\infty\).
  • Score of the best alignment between A0 and Bj that results a gap in B. Not possible, hence, First row of A is initialized with - \(\infty\).

Overlap alignment

A 0 1 2 3 4 5
0 - \(\infty\) - \(\infty\) - \(\infty\) - \(\infty\) - \(\infty\) - \(\infty\)
1 0
2 0
3 0
B 0 1 2 3 4 5
0 - \(\infty\) 0 0 0 0 0
1 - \(\infty\)
2 - \(\infty\)
3 - \(\infty\)

Non-overlap alignment

A 0 1 2 3 4 5
0 - \(\infty\) - \(\infty\) - \(\infty\) - \(\infty\) - \(\infty\) - \(\infty\)
1 -22
2 -29
3 -36
B 0 1 2 3 4 5
0 - \(\infty\) -22 -29 -36 -43 -50
1 - \(\infty\)
2 - \(\infty\)
3 - \(\infty\)