Publications - Published papers

Please find below publications of our group. Currently, we list 508 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

RNAstrand: Reading Direction of Structured RNAs in Multiple Sequence Alignments

Kristin Missal, Peter F. Stadler


PREPRINT 06-006: [ PDF ]
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Alg.Mol.Biol. 2:6 (2007)


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. While folding energies of an RNA and its reverse complement are similar, the difference are sufficient at least in conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here a support vector machine (SVM) that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment.


ncRNA genes, reading direction, support vector machine