A method for assessing the statistical significance of RNA folding.

Journal of Theoretical Biology
S Y Le, J V Maizel

Abstract

We have developed a statistical method that is designed for analyzing potential RNA folded substructures. The statistical significance of RNA folding is assessed by the segment score. The segment score is defined as the difference between the lowest free energy calculated for the real biological sequence and the mean of the lowest free energies from random permutations of the real segment sequence, divided by the standard deviation of the random sample. This procedure was applied to the well-studied Escherichia coli 16S rRNA and potato spindle tuber viroid (PSTV) RNA. The results showed that the predictions of the locally significant secondary structures in these two molecules are in accord with the universally conserved local secondary structure elements (Gutell, Weiser & Noller, 1985, Prog. Nucl. Acid Res. molec. Biol. 32, 155-216; Riesner & Gross, 1985, A. Rev. Biochem. 54, 531-564). In addition, a statistical analysis indicated that the lowest free energies of a random sample set follow an approximately normal distribution. A reasonable size for the random sample set was determined statistically. Moreover, the statistical evaluation has been carried out using three different sets of energy rules--two sets (Salser, 1977, Col...Continue Reading

Citations

Nov 1, 1991·Genetic Analysis, Techniques and Applications·S Y LeJ V Maizel
Feb 13, 2001·Gene·D R Forsdyke, J R Mortimer
Jun 14, 2000·Current Opinion in Structural Biology·M Zuker
Mar 16, 2011·The Journal of Biological Chemistry·Daniel R BoutzLuiz O F Penalva
Aug 25, 1995·Nucleic Acids Research·B SchmidH U Göringer
Oct 7, 2008·Nucleic Acids Research·Matthias MüllnerStanislav Indik
Mar 26, 2010·BMC Bioinformatics·Feng-Jie Sun, Gustavo Caetano-Anollés
Oct 6, 2005·BMC Bioinformatics·Eva FreyhultVincent Moulton
Aug 30, 2008·PLoS Computational Biology·Miler T Lee, Junhyong Kim
Apr 4, 1997·The Journal of Biological Chemistry·J BernsteinO Elroy-Stein
Jan 24, 2018·Nucleic Acids Research·Katrina M KutchkoAlain Laederach
Oct 31, 2003·The Journal of Biological Chemistry·Rachel KilavTally Naveh-Many
Jan 15, 2021·Proceedings of the National Academy of Sciences of the United States of America·Mark N RaghebHoura Merrikh

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