RNAstrand: reading direction of structured RNAs in multiple sequence alignments

MOTIVATION: Genome-wide screens for structured ncRNA genes in mammals, urochordates, and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional annotation is to determine the reading direction with high precision. RESULTS: While folding energies of an RNA and its reverse complement are similar, the differences are sufficient at least in conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here a support vector machine that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment and provides a considerable improvement in classification accuracy over previous approaches. SOFTWARE: RNAstrand is freely available as a stand-alone tool from and is also included in the latest release of RNAz, a part of the Vienna RNA Package.