Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach

In addition to the well-known edit operations, the alignment of minisatellite maps includes duplication events. We model these duplications using a special kind of spanning trees and deduce an optimal duplication scenario by computing the respective minimum spanning tree. Based on best duplication scenarios for all substrings of the given sequences, we compute an optimal alignment of two minisatellite maps. Our algorithm improves upon the previously developed algorithms in the generality of the model, in alignment quality and in space-time efficiency. Using this algorithm, we derive evidence that there is a directional bias in the growth of minisatellites of the MSY1 dataset.