Global Alignment Problems

Anyone familiar with global alignment problems? It's a big thing in Bioinformatics (although mostly a Math course). I have a couple I could use some help on dealing with "gaps," optimal alignments, and so forth. They're generally in the form of boxes, with arrows from one box to the next depending on the penalties. I could express this as a matrix in trying to illustrate the alignment matrix, although trying to also indicate the arrows (right, down, diagonal) would be tough, but I could prob. find a way. Before I even attempt giving the questions, I was wondering if anyone had knowledge of this area, since it's relatively new.

Thanks.