CARNA--alignment of RNA structure ensembles.

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 ou

SUBMITTER: Sorescu DA 

PROVIDER: S-EPMC3394245 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature