Publications - Published papers

Please find below publications of our group. Currently, we list 53 papers. Some of the publications are in collaboration with the group of Peter Stadler and are also listed in the publication list for his group. Access to published papers (access) is restricted to our local network and chosen collaborators.
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Protein-Coding Structured RNAs
A Computational Survey of Conserved RNA Secondary Structures Overlapping Coding Regions in Drosophilids

Sven Findeiß, Jan Engelhardt, Sonja J. Prohaska and Peter F. Stadler


PREPRINT 11-012: [ PDF ]  [ Supplement ]




Functional RNA elements can be embedded also within exonic sequences coding for functional proteins. While not uncommon in viruses, only a few examples of this type have been described in some detail for eukaryotic genomes. Here we use RNAz and RNAcode, two comparative genomics methods that measure signatures of stabilizing selection acting on RNA secondary structure and peptide sequence, resp., to survey the fruitfly genomes. We estimate that there might be on the order of 1000 loci that are subject to dual selection pressure. The used genome-wide screens also expose the limitations of the currently available methods.


dual RNAs, RNA secondary structures, coding sequence, RNAz, RNAcode