Forest alignment with affine gaps and anchors

Abstract

We present two enhancements to Jiang's tree alignment algorithm, motivated by experience with its use for RNA structure alignment. One enhancement is the introduction of an affine gap model, which can be accommodated with a runtime increase by a constant factor. The second enhancement is a speed-up of the alignment algorithm when certain nodes in the trees are pre-aligned by a so-called anchoring. Both enhancements are included in a new implementation of the tool RNAforester. We also argue that tree alignment should be parameterized by a user-described set of edit operations, generalizing over the traditional, atomic edit operations. © 2011 Springer-Verlag.