Forest Alignment with Affine Gaps and Anchors

  • Stefanie Schirmer
  • Robert Giegerich
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6661)

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.

Keywords

RNA structure alignment forest alignment affine gap costs anchored alignment 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Stefanie Schirmer
    • 1
  • Robert Giegerich
    • 1
  1. 1.Practical Computer ScienceBielefeld UniversityBielefeldGermany

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