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mco1321301839.pdf (2.41 MB)
ETD Abstract Container
Abstract Header
Evolution and Function of Compositional Patterns in Mammalian Genomes
Author Info
Prakash, Ashwin
Permalink:
http://rave.ohiolink.edu/etdc/view?acc_num=mco1321301839
Abstract Details
Year and Degree
2011, Doctor of Philosophy (PhD), University of Toledo, College of Medicine.
Abstract
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.
Committee
Alexei Fedorov, PhD (Committee Chair)
Joseph Shapiro, MD (Committee Member)
Deepak Malhotra, MD, PhD (Committee Member)
Robert Trumbly, PhD (Committee Member)
Sadik Khuder, PhD (Committee Member)
Pages
186 p.
Subject Headings
Bioinformatics
;
Biomedical Research
;
Genetics
;
Medicine
;
Molecular Biology
Keywords
Genomic Mid range inhomogeneity
;
GMRI
;
MRI
;
introns
;
ncRNA
;
DNA conformations
;
ZDNA
;
HDNA
;
RNA secondary structures
;
miRNA
;
Long non coding RNA
;
piRNA
;
siRNA
;
snoRNA
;
Orthologous introns
;
Database of orthologous mammalian introns
;
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Citations
Prakash, A. (2011).
Evolution and Function of Compositional Patterns in Mammalian Genomes
[Doctoral dissertation, University of Toledo]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=mco1321301839
APA Style (7th edition)
Prakash, Ashwin.
Evolution and Function of Compositional Patterns in Mammalian Genomes.
2011. University of Toledo, Doctoral dissertation.
OhioLINK Electronic Theses and Dissertations Center
, http://rave.ohiolink.edu/etdc/view?acc_num=mco1321301839.
MLA Style (8th edition)
Prakash, Ashwin. "Evolution and Function of Compositional Patterns in Mammalian Genomes." Doctoral dissertation, University of Toledo, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=mco1321301839
Chicago Manual of Style (17th edition)
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Document number:
mco1321301839
Download Count:
599
Copyright Info
© 2011, all rights reserved.
This open access ETD is published by University of Toledo Health Science Campus and OhioLINK.