Partially Local Multi-Way Alignments

Abstract,  With increasing computational resources exact solutions to 3- and 4-way alignments have become feasible in practise. In the pairwise case there is a clear distinction between local and global alignments. As more sequences considered this distinction, which can in fact be made independently for both ends of each sequence, gives rise to a rich set of partially local alignments. So far these
have remained largely unexplored. Here we propose a very general framework for this class of problems and show how exact dynamic programming solutions can be constructed in principled manner.