Multiple Structural RNA Alignment with Lagrangian Relaxation

In contrast to proteins, 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, structurebased, multiple RNA alignments and give an algorithm that finds such an optimal solution or at least a very good approximation of it. Our formulation is based on the structural trace formulation of Reinert et al. and uses a recently proposed weighting function of Hofacker et al. that makes use of McCaskill’s approach to compute base pair probability functions. To solve the resulting computational problem we propose an algorithm ...

• Type: Conference
• Year: 2005
• Where: WABI
• Authors: Markus Bauer, Gunnar W. Klau, Knut Reinert
• Keywords: Algorithms, Multiple Alignments, Multiple Rna Alignments, Multiple Structural Alignments, WABI 2005