Publications - Published papers
Please find below publications of our group. Currently, we list 565 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 (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) 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.
Temperature-Dependent Structural Variability of RNAs: Spliced Leader RNAs and their Evolutionary History
Manja Marz, Nathalie Vanzo, Peter F. Stadler
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Status: Published
J Bioinform Comput Biol. 8: 1-17 (2010)
Abstract
The structures attained by RNA molecules depend not only on their
sequence but also on environmental parameters such as their structure.
So far, this effect has been largely neglected in bioinformatics
studies. Here we show that structural comparisons can be facilitated
and more coherent structural models can be obtained when differences in
environmental parameters are taken into account. We re-evaluate the
secondary structures of the spliced leader RNAs from the seven
eukaryotic phyla in which SL RNA \emph{trans}-splicing has been
described. Adjusting structure prediction to the natural growth
temperatures and considering energetically similar secondary structures
we observe striking similarities among Euglenida, Kinetoplastida,
Dinophyceae, Cnidaria, Rotifera, Nematoda, Platyhelminthes, and
Tunicata that cannot be explained easily by the independent innovation
of SL RNAs in each of these phyla.
Keywords
RNA folding; temperature dependence; SL RNA; trans-splicing; evolution