Pairwise Alignment

The lecture introduces the problem of comparing two sequences while allowing certain mismatches between the two. The problem will be referred to as (pairwise) sequence alignment. or inexact matching. We first present the problem and provide biological motivation. We then define similarity and difference between sequences and present algorithms for computing them, with analysis of the complexity of these algorithms. The algorithms use the dynamic programming technique. For each algorithm the following information will be given:

• Intuitive explanation of the recursive process.
• Formal definition of the recursive process.
• Discussion of the complexity.