Hey everyone! I am having a little difficulty trying to figure out how to align two sequences in Python using a Dynamic Programming algorithm. I've tried to take a look at the source code for jAligner, but I'm having issues understanding how it works.
Basically the problem is this:
Given two sequences, a scoring matrix given that gives scores between each nucleotide, a start gap penalty, and a continue gap penalty. For example:
A G C T A 1 -2 -2 -1 G -2 1 -1 -2 C -2 -1 1 -5 T -1 -2 -2 1 openGap = -3 continueGap = -1
How do we compute the alignment of two sequences A and B (with length N and M) such that the score is maximized?
I've taken a look at This Wikipedia Page, but it doesn't mention anything about a continue/open gap, rather just one single gap score.