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Structural genomics meets phylogenetics and vice versa: Knowing rRNA secondary structures is a prerequisite for constructing rRNA alignments for inferring phylogenies, and inferring phylogenies is a precondition to understand the evolution of such rRNA secondary structures. Here, both scientific worlds go together. The rRNA internal transcribed spacer 2 (ITS2) region is a widely used phylogenetic marker. Because of its high variability at the sequence level, correct alignments have to take into account structural information. In this study, we examine the extent of the conservation in structure. We present (1) the homology modeled secondary structure of more than 20,000 ITS2 covering about 14,000 species; (2) a computational approach for homology modeling of rRNA structures, which additionally can be applied to other RNA families; and (3) a database providing about 25,000 ITS2 sequences with their associated secondary structures, a refined ITS2 specific general time reversible (GTR) substitution model, and a scoring matrix, available at http://its2.bioapps.biozentrum.uni-wuerzburg.de.

Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures