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GENOMIC MAPPING: A STATISTICAL AND ALGORITHMIC ANALYSIS OF
THE OPTICAL MAPPING SYSTEM
by
John Vu Nguyen
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(COMPUTATIONAL BIOLOGY AND BIOINFORMATICS)
May 2010
Copyright 2010 John Vu Nguyen
Object Description
| Title | Genomic mapping: a statistical and algorithmic analysis of the optical mapping system |
| Author | Nguyen, John Vu |
| Author email | jvnguyen@usc.edu; jvnguyen@gmail.com |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Computational Biology & Bioinformatics |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2009-08-21 |
| Date submitted | 2010 |
| Restricted until | Unrestricted |
| Date published | 2010-01-27 |
| Advisor (committee chair) | Waterman, Michael S. |
| Advisor (committee member) |
Sun, Fengzhu Z. Li, Lei M. Kempe, David |
| Abstract | The ability to conduct whole genome analysis of variation is slowly becoming a reality with both improvements in biotechnology and advancements in data analysis. However, large-scale de novo sequencing still remains a formidable task for complex plant and mammalian genomes. Although not providing resolution at the sequence nucleotide level, physical maps convey useful information that can be leveraged to discover biological events not possible with sequencing technologies. Optical mapping, a novel restriction mapping technology, is able to produce complete genome-wide physical maps both quickly and cheaply. These maps serve not only as invaluable aids for de novo sequencing, but can be used directly to make valuable inferences regarding the underlying genome itself. However, in order for optical mapping to be useful as a tool for genomic analysis, both computational and statistical questions must be addressed. In this thesis, we explore some of the issues involved with analyzing optical mapping data. Specifically, we explore various statistical models and their implications for optical mapping data. We also develop a new scoring function for the alignment of optical maps using dynamic programming. A strategy for comparing optical mapping data against a clone-based sequencing strategy for a genome is examined. Finally, methods for assembling optical mapping data into a complete genome-wide physical map are presented. |
| Keyword | genomic mapping; optical map alignment; optical map assembly; optical mapping |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m2815 |
| Contributing entity | University of Southern California |
| Rights | Nguyen, John Vu |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | cisadmin@dots.usc.edu |
| Filename | etd-Nguyen-3472 |
| Archival file | uscthesesreloadpub_Volume29/etd-Nguyen-3472.pdf |
Description
| Title | Page 1 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@dots.usc.edu |
| Full text | GENOMIC MAPPING: A STATISTICAL AND ALGORITHMIC ANALYSIS OF THE OPTICAL MAPPING SYSTEM by John Vu Nguyen A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (COMPUTATIONAL BIOLOGY AND BIOINFORMATICS) May 2010 Copyright 2010 John Vu Nguyen |
