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Optimizing Approaches for Sensitive, High Performance Clustering of Gene Expressions

Moler, James C.
http://rave.ohiolink.edu/etdc/view?acc_num=miami1303482998

Abstract Details

2011, Master of Science, Miami University, Computer Science and Systems Analysis.
This thesis presents several new algorithmic approaches to the problem of clustering conventional ESTs and high throughput gene expression data, which are implemented in the software tool PEACE. The d2 algorithm for sequence comparison is improved and enhanced with a novel two-pass extension, and a minimum spanning tree-based algorithm is used to cluster ESTs, providing an efficient and accurate solution. Furthermore, in order to address the unique challenges of high throughput sequencing technologies such as 454, Illumina and SOLiD sequencing, an adaptive d2 algorithm is introduced to handle variations in fragment length. The resulting tool compares favorably with other leading tools in the literature, including WCD, CAP3, and TGICL, on both EST and next-generation sequencing (NGS) data.
John Karro, PhD (Advisor)
Dhananjai Rao, PhD (Committee Member)
Mufit Ozden, PhD (Committee Member)
40 p.
Bioinformatics; Computer Science
clustering gene expressions; EST

Recommended Citations

Citations

  • Moler, J. C. (2011). Optimizing Approaches for Sensitive, High Performance Clustering of Gene Expressions [Master's thesis, Miami University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=miami1303482998

    APA Style (7th edition)

  • Moler, James. Optimizing Approaches for Sensitive, High Performance Clustering of Gene Expressions. 2011. Miami University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=miami1303482998.

    MLA Style (8th edition)

  • Moler, James. "Optimizing Approaches for Sensitive, High Performance Clustering of Gene Expressions." Master's thesis, Miami University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=miami1303482998

    Chicago Manual of Style (17th edition)

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This open access ETD is published by Miami University and OhioLINK.