I'm new to bioinformatics and I've recently stumbled across the Nussinov-Jacobson algorithm, which confused me quite a bit. It's rather difficult to understand in my opinion. However, what I do understand is that:
You fill out the first diagonal with zero for nucleotides that do not match with itself.
If they do match, we score them 1.
Now comes the triggy part. When we fill out the rest of the matrix, we have to take the "k-value" into account. What does the k-value even mean and how do we add that value into our matrix? Please, help me. I'm so confused, guys.
Thanks in advance!