Multiple Structural RNA Alignment with Lagrangian Relaxation

  • Markus Bauer
  • Gunnar W. Klau
  • Knut Reinert
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3692)


Many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence, it is clear that any method that relates RNA sequences in form of (multiple) alignments should take structural features into account. Since multiple alignments are of great importance for subsequent data analysis, research in improving the speed and accuracy of such alignments benefits many other analysis problems.

We present a formulation for computing provably optimal, structure-based, multiple RNA alignments and give an algorithm that finds such an optimal (or near-optimal) solution. To solve the resulting computational problem we propose an algorithm based on Lagrangian relaxation which already proved successful in the two-sequence case. We compare our implementation, mLARA, to three programs (clustalW, MARNA, and pmmulti) and demonstrate that we can often compute multiple alignments with consensus structures that have a significant lower minimum free energy term than computed by the other programs. Our prototypical experiments show that our new algorithm is competitive and, in contrast to other methods, is applicable to long sequences where standard dynamic programming approaches must fail. Furthermore, the Lagrangian method is capable of handling arbitrary pseudoknot structures.


Lagrangian Relaxation Minimum Free Energy Consensus Structure Lagrangian Problem Consensus Secondary Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Markus Bauer
    • 1
    • 2
  • Gunnar W. Klau
    • 3
  • Knut Reinert
    • 1
  1. 1.Institute of Computer ScienceFree University of BerlinGermany
  2. 2.International Max Planck Research School for Computational Biology and Scientific Computing 
  3. 3.Institute of MathematicsFree University of BerlinGermany

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