TBI-p-2012-3
Download:
Titel:
CARNA - Alignment of RNA Structure Ensembles
Author(s):
Alexandru Sorescu, Mathias Möhl, Martin Mann, Rolf Backofen, and Sebastian Will
submitted to:
Abstract:
Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool CARNA. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large exibility in the input, ranging from xed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, CARNA optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared to already costly Sankoff-style alignment, CARNA solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although CARNA is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA.
Link to publication:
Return to Index
Return to List
Last modified: 2008-10-22 12:23:11 fall