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Xiaolin Liu_dissertation.pdf (2.53 MB)

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Novel bioinformatics tools for elementary repeat assembly, repeat domain discovery, and TE-based analysis of substitution rates

Liu, Xiaolin
http://orcid.org/0000-0002-1753-2551
http://rave.ohiolink.edu/etdc/view?acc_num=miami1525308930990689

Abstract Details

2018, Doctor of Philosophy, Miami University, Cell, Molecular and Structural Biology (CMSB).
Transposable elements, elements inserted into the genome by repeated copying of some ancestral sequences and their descendants, are present in almost every eukaryote genome. Since their discovery, it has become clear that they have had a fundamental impact on the structure, organization and evolution of their host genomes. The research objective of this work centers around the identification and use of transposable elements (TE), with the ultimate aim of producing new software tools that will expedite TE-based biological research. In Chapter 2, we tackle the algorithmic problems associated with de novo discovery and annotation of transposable elements, as well as implement the Elementary Repeat Assembly tool around the algorithm, which will allow for the quick identification of transposable elements of a newly sequenced genome without requiring the construction of a RepBase library for the genome. In Chapter 3, we implement an algorithm for the automatic identification of repeat domains from large genomes, construct the Repeat Domain Discovery (RDD) tool and demonstrate its capabilities to detect repeat domains de novo from genomic sequences. In addition, we devise a new approach for building the phylogenetic tree from information provided by the repeat domain structure. In Chapter 4, we establish a novel, verified method (through exploration of our new genomic repeats annotation tools) for generating data useful in genomic-wide substitution rate analysis, conducting the first such studies in plant genomes using single-species approach. The research of substitution rates in plants serves a proof of concept, paving the way to developments of more general computational tools for genomic analysis.
John Karro (Advisor)
127 p.
Bioinformatics
elementary repeat assembly, repeat domain, substitution rates

Recommended Citations

Citations

  • Liu, X. (2018). Novel bioinformatics tools for elementary repeat assembly, repeat domain discovery, and TE-based analysis of substitution rates [Doctoral dissertation, Miami University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=miami1525308930990689

    APA Style (7th edition)

  • Liu, Xiaolin. Novel bioinformatics tools for elementary repeat assembly, repeat domain discovery, and TE-based analysis of substitution rates. 2018. Miami University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=miami1525308930990689.

    MLA Style (8th edition)

  • Liu, Xiaolin. "Novel bioinformatics tools for elementary repeat assembly, repeat domain discovery, and TE-based analysis of substitution rates." Doctoral dissertation, Miami University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=miami1525308930990689

    Chicago Manual of Style (17th edition)

miami1525308930990689
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© 2018, some rights reserved.Creative Commons License Novel bioinformatics tools for elementary repeat assembly, repeat domain discovery, and TE-based analysis of substitution rates by Xiaolin Liu is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by Miami University and OhioLINK.