title: Local thermodynamic stability scores are well represented by a non-central student's t distribution.
abstract: Local folding in mRNAs is closely associated w ith biological functions. In this study, we reveal the whole distribution of local thermodynamic stability in the complete genome of the poliovirus P3/Leon/37 and the single-stranded RNA sequences that corresponds to the nucleotide sequence of the complete genome sequence (1 667 867 bp) of Helicobacter pylori (H. pylori) strain 26695. Local thermodynamic stability in the RNA sequences is measured by two standard z -scores, significance score and stability score. To estimate the distribution of thermodynamic stability, a model based on the non-central Student's t distribution has been developed. Significant patterns of extremes that are either much more stable or unstable than expected by chance are detected. Our results indicate that the highly stable and statistically more significant folding regions are predominantly in non-coding sequences in the two genome sequences. Moreover, the highly unstable folding regions, on the contrary, are predominantly in the protein coding sequences of H. pylori. The observed differences across the complete genomic sequences are statistically very significant by a chi2-test. These extreme patterns may be useful in searching for target sequences for long-chain antisense RNA and for locating potential RNA functional elements involved in the regulation of gene expression including translation, mRNA localization and metabolism.
authors.affiliation: Laboratory of Experimental and Computational Biology, Division of Basic Sciences, National Cancer Institute, NIH, Bldg 469, Room 151, Frederick, MD 21702, USA. shuyun@orleans.ncifcrf.gov
authors.forename: S Y
authors.initials: SY
authors.lastname: Le
authors.forename: W M
authors.initials: WM
authors.lastname: Liu
authors.forename: J H
authors.initials: JH
authors.lastname: Chen
authors.forename: J V
authors.initials: JV
authors.lastname: Maizel
mesh_terms: D000818:Animals; D016009:Chi-Square Distribution; D019295:Computational Biology; D005798:Genes, Bacterial; D005814:Genes, Viral; D016480:Helicobacter pylori / Q000235:genetics*; D015233:Models, Statistical; D017955:Poliovirus / Q000235:genetics*; D012333:RNA, Messenger / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D012333:RNA, Messenger