Thermodynamic matchers: strengthening the significance of RNA folding energies

Höchsmann T, Höchsmann M, Giegerich R (2006)
Comput Syst Bioinformatics Conf.

Journal Article | Published | English

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Thermodynamic RNA secondary structure prediction is an important recipe for the latest generation of functional non-coding RNA finding tools. However, the predicted energy is not strong enough by itself to distinguish a single functional non-coding RNA from other RNA. Here, we analyze how well an RNA molecule folds into a particular structural class with a restricted folding algorithm called Thermodynamic Matcher (TDM). We compare this energy value to that of randomized sequences. We construct and apply TDMs for the non-coding RNA families RNA I and hammerhead ribozyme type III and our results show that using TDMs rather than universal minimum free energy folding allows for highly significant predictions.
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Höchsmann T, Höchsmann M, Giegerich R. Thermodynamic matchers: strengthening the significance of RNA folding energies. Comput Syst Bioinformatics Conf. 2006.
Höchsmann, T., Höchsmann, M., & Giegerich, R. (2006). Thermodynamic matchers: strengthening the significance of RNA folding energies. Comput Syst Bioinformatics Conf.
Höchsmann, T., Höchsmann, M., and Giegerich, R. (2006). Thermodynamic matchers: strengthening the significance of RNA folding energies. Comput Syst Bioinformatics Conf.
Höchsmann, T., Höchsmann, M., & Giegerich, R., 2006. Thermodynamic matchers: strengthening the significance of RNA folding energies. Comput Syst Bioinformatics Conf.
T. Höchsmann, M. Höchsmann, and R. Giegerich, “Thermodynamic matchers: strengthening the significance of RNA folding energies”, Comput Syst Bioinformatics Conf, 2006.
Höchsmann, T., Höchsmann, M., Giegerich, R.: Thermodynamic matchers: strengthening the significance of RNA folding energies. Comput Syst Bioinformatics Conf. (2006).
Höchsmann, Thomas, Höchsmann, Matthias, and Giegerich, Robert. “Thermodynamic matchers: strengthening the significance of RNA folding energies”. Comput Syst Bioinformatics Conf (2006).
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2 Citations in Europe PMC

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Thermodynamic matchers for the construction of the cuckoo RNA family.
Reinkensmeier J, Giegerich R., RNA Biol 12(2), 2015
PMID: 25779873
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti.
Schluter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Janicke S, Becker JD, Giegerich R, Becker A., BMC Genomics 11(), 2010
PMID: 20398411

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