Degree Type

Dissertation

Date of Award

2007

Degree Name

Doctor of Philosophy

Department

Theses & dissertations (Interdisciplinary)

Major

Bioinformatics and Computational Biology

First Advisor

Srinivas Aluru

Second Advisor

Patrick S. Schnable

Abstract

Concurrent advances in high-throughput sequencing and assembly have led to the completion of many complex genomes. Even so, these assemblies require substantial computational resources. In this dissertation, we present a massively parallel approach that scales to thousands of processors without duplicating the biological expertise present in conventional assembly software.;Additional bioinformatics techniques were required to accurately assemble the maize genome including novel repeat detection, and the resulting framework has been strongly supported by maize experimental data. More recently, this framework has been generalized for fruit fly, sorghum, soybean and environmental sequence assemblies.;Questions in plant genome analysis were also addressed. For example, we have discovered an estimated 350 "orphan" maize genes and have shown that approximately 1% of all maize genes were recently duplicated, many of which into at least two functional copies. LCM-454 sequencing is introduced and analyses that indicate this approach can discover rare, potentially tissue-specific transcripts and thousands of SNPs will be presented.;This dissertation combines high performance computing, computational biology and high-throughput sequencing for our ongoing work on the maize genome project. We conclude by describing how these contributions can be useful for any species, including non-model organisms that are unlikely to be fully sequenced.

DOI

https://doi.org/10.31274/rtd-180813-16750

Publisher

Digital Repository @ Iowa State University, http://lib.dr.iastate.edu/

Copyright Owner

Scott Joseph Emrich

Language

en

Proquest ID

AAI3274894

OCLC Number

182858018

ISBN

9780549154914

File Format

application/pdf

File Size

168 pages

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