RNAstrand predicts the reading direction of a structured RNA gene from a multiple sequence alignment and its reverse complement. It is meant as a post processing tool for RNA prediction tools which in general do not reliable annotate the reading direction of the structured RNA candidate.
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RNAstrand: Reading direction of structured RNAs in multiple sequence alignments
Kristin Reiche, Peter F. Stadler,
Algorithms for Molecular Biology, 2:6, 2007.