Genomic data analysis using DNA structure: an analysis of conserved nongenic sequences and ultraconserved elements.
Recent comparative studies of the human and mouse genomes have revealed sets of conserved nongenic sequences (CNGs) and sets of ultraconserved elements (UCEs). Both sets of sequences, which exhibit extremely high levels of conservation, extend over hundreds of bases and have no known function. Since there is no detectable sequence homology between paralogous CNGs or UCEs in either of the species, an alignment-free technique is needed for their analysis. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers, including information on stability, the minimum energy conformation, and flexibility. We have used Fourier techniques to analyze the UCEs and CNGs in terms of their octamer structural properties, to reveal structural correlations which may indicate possible functions for some of these sequences.
Gardiner
Eleanor J
EJ
Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom. e.gardiner@sheffield.ac.uk
Hirons
Linda
L
Hunter
Christopher A
CA
Willett
Peter
P
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics*; D021901:DNA, Intergenic / Q000737:chemistry* / Q000235:genetics*; D005583:Fourier Analysis; D023281:Genomics / Q000379:methods*; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008969:Molecular Sequence Data
D021901:DNA, Intergenic