title: Discovering well-ordered folding patterns in nucleotide sequences.
abstract: BACKGROUND
  Growing evidence demonstrates that local well-ordered structures are closely correlated with cis-acting elements in the post-transcriptional regulation of gene expression. The prediction of a well-ordered folding sequence (WFS) in genomic sequences is very helpful in the determination of local RNA elements with structure-dependent functions in mRNAs.
  
  
  RESULTS
  In this study, the quality of local WFS is assessed by the energy difference (E(diff)) between the free energies of the global minimal structure folded in the segment and its corresponding optimal restrained structure (ORS). The ORS is an optimal structure under the condition in which none of the base-pairs in the global minimal structure is allowed to form. Those WFSs in HIV-1 mRNA, various ferritin mRNAs and genomic sequences containing let-7 RNA gene were searched by a novel method, ed_scan. Our results indicate that the detected WFSs are coincident with known Rev response element in HIV-1 mRNA, iron-responsive elements in ferritin mRNAs and small let-7 RNAs in Caenorhabditis elegans, Caenorhabditis briggsae and Drosophila melanogaster genomic sequences. Statistical significance of the WFS is addressed by a quantitative measure Zscr(e) that is a z-score of E(diff) and extensive random simulations. We suggest that WFSs with high statistical significance have structural roles involving their sequence information.
  
  
  BACKGROUND
  The source code of ed_scan is available via anonymous ftp as ftp://ftp.ncifcrf.gov/pub/users/shuyun/scan/ed_scan.tar.
authors.affiliation: Laboratory of Experimental and Computational Biology, NCI Center for Cancer Research, National Cancer Institute, NIH, Bldg 469, Room 151, Frederick, MD 21702, USA. shuyun@orleans.ncifcrf.gov
authors.forename: Shu-Yun
authors.initials: SY
authors.lastname: Le
authors.forename: Jih-H
authors.initials: JH
authors.lastname: Chen
authors.forename: Danielle
authors.initials: D
authors.lastname: Konings
authors.forename: Jacob V
authors.initials: JV
authors.lastname: Maizel
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D005293:Ferritins / Q000737:chemistry / Q000235:genetics; D005786:Gene Expression Regulation; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger; D005293:Ferritins