Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization

14 years 5 months ago

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During the last few years new functionalities of RNA have been discovered, renewing the need for computational tools for their analysis. To this respect, multiple sequence alignment is an essential step in ﬁnding structurally conserved regions in related RNA sequences. 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, any method that relates RNA sequences in form of multiple alignments should take structural features into account, which has been veriﬁed in recent studies. Progress has been made in developing new structural alignment algorithms, however, current methods are computationally costly or do not have the desired accuracy to make them an everyday tool. In this paper we present a fast, practical, and accurate method for computing multiple, structural RNA alignments. The method is based on combining a new pairwise structural alignment method with...

Markus Bauer, Gunnar W. Klau, Knut Reinert

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