The alignment returned by nwalign is a 3xN character array showing the optimal alignment between the two input protein sequences. The first row is the first input sequence, the middle row shows alignment information, and the last shows the second sequence:
>> al(:,1:10)
ans =
3×10 char array
'QKQEIKMNPN'
' ||||'
'------MNPN'
We then use seqinsertgaps to get the original nucleotide sequence, but with the gap information returned by the alignment, so the inputs are the first and third rows of the alignment character vector.
