Thesis
Computational approaches for comparative genomics and transcriptomics using 454 sequencing technology
Washington State University
Master of Science (MS), Washington State University
2009
Handle:
https://hdl.handle.net/2376/103774
Abstract
The development and application of computational tools has consistently played an integral role in the advancement of genomics research, leading to the sequencing, assembly and annotation of hundreds of genomes over the last two decades. However, over the last two years, the research community has embraced an array of new high-throughput, cost-effective technologies, referred to as the "next-generation sequencing technologies" , which are poised to alter the landscape of genomics research in the path to accelerated biological discovery. This imminent scientific revolution can, however, happen only if a) new computational tools are developed to cater to the type of data generated by these new technologies; and b) efficient computational frameworks are implemented to seamlessly integrate both new and old tools and enable biologists to answer domain-specific questions. The goal of this thesis is to address the latter need in the context of two projects — one toward the sequencing the genome of a new extremophile microbe and another toward enabling transcriptomics in tree fruit species for which the underlying genomics is not yet fully understood. Both projects use the 454 sequencing technology, which is one of the next-generation sequencing technologies. More specifically, the contributions of the thesis are in the development and application of computational frameworks that have led to the generation of the first known 454-sequencing based draft assembly of the Sulfolobus solfataricus strain 98/2 genome along with its comparative genomics, and to the enabling of 454-sequencing based transcriptomics characterization of apple, pear and cherry. It is expected that the methods and computational frameworks implemented as part of this thesis will have a broader applicability in the near future for projects in comparative genomics and transcriptomics that use next-generation sequencing technologies. The thesis is the result of the collaboration among the WSU Department of Horticulture, WSU School of Molecular Biosciences and the WSU School of EECS.
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Details
- Title
- Computational approaches for comparative genomics and transcriptomics using 454 sequencing technology
- Creators
- Vandhana Krishnan
- Contributors
- Ananth Kalyanaraman (Degree Supervisor)
- Awarding Institution
- Washington State University
- Academic Unit
- Electrical Engineering and Computer Science, School of
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University; Pullman, Wash. :
- Identifiers
- 99900525059501842
- Language
- English
- Resource Type
- Thesis