The protein coding sequences of humans and of most mammals represent less than 2% of their genomes. The remaining 98% is made up of 5'- and 3'-untranslated regions of mRNAs (<2%), introns (∼30%), and intergenic regions (∼66%).These vast non-protein coding genomic areas, previously frequently referred to as "junk" DNA, contain numerous functional signals of various origin and purpose. The presence of functional information within these vast non-protein coding regions creates function dependent compositional variations. The traditional techniques for mining functional regions have focused mainly on comparative methods where strong sequence similarity of genomic regions between evolutionarily distant species, was deemed to be indicative of a fixation bias in order to maintain functional integrity. In this study we present a novel method of mining functional regions which range in length from 30 nucleotides to several thousands of nucleotides, which we call Mid-Range scale or Mid-Range Inhomogeneity (MRI / genomic MRI). The focus of this study is to demonstrate that at these mid-range scales, genomes of complex eukaryotes consist of a number of different nucleotide compositional patterns which are associated with unusual DNA conformations, RNA secondary structures and non-coding RNA. Some of these patterns are scarcely investigated and still await thorough exploration and recognition.
|Commitee:||Khuder, Sadik, Malhotra, Deepak, Shapiro, Joseph, Trumbly, Robert|
|School:||The University of Toledo|
|Department:||College of Medicine|
|School Location:||United States -- Ohio|
|Source:||DAI-B 73/05, Dissertation Abstracts International|
|Subjects:||Genetics, Medicine, Bioinformatics|
|Keywords:||Compositional patterns, Dna conformations, Genomic mid range inhomogeneity, Hdna, Introns, Mammalian genomes, Non coding rna, Zdna|
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