RNAstrand: reading direction of structured RNAs in multiple sequence alignments

RNAstrand predicts the reading direction of a structured RNA in a multiple sequence alignment by employing a support vector machine (SVM):

Example

Reading strand information is given in the small asymmetry in the energy rules and in particular by GU pairs that map to a non-canonical AC pair in the reverse complement of the alignment. Those asymmetries are utilized by four classification variables: The energetic differences between strands are captured by the differences of z-scores and mean folding energies, while the differences in structure conservation are described by the differences in structural conservation (SCI) and consensus energies. The output is a score D which converges to +1 the larger the evidence that RNA is in reading direction of input alignment and to -1 the larger the evidence that RNA is in reverse complement of input alignment. Classification is reported according to a threshold value c:
  1. D > +c: RNA is in reading direction of input alignment
  2. D < -c: RNA is reverse complement of input alignment
  3. -c <= D <= +c: No decision of reading direction

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Updated: 29 May 2007