Skip to Main Content
 

Global Search Box

 
 
 

ETD Abstract Container

Abstract Header

Using Weighted Set Cover to Identify Biologically Significant Motifs

Schmidt, Robert J.M.
http://orcid.org/0000-0002-3619-3559
http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1447797982

Abstract Details

2015, Master of Science (MS), Ohio University, Computer Science (Engineering and Technology).
One of the greatest challenges of mankind is understanding how living organisms operate, and a key step towards understanding this challenge is identifying how genes are regulated. Promoter regions play a key role in the regulation of genes via sequences of DNA base pairs known as transcription factor binding sites. When a transcription factor binding site is activated, the genes associated with the transcription factor binding site are transcribed, the first step towards creating proteins. The identification of transcription factor binding sites has come a long way with the advancements of next generation sequencing technologies and projects like ENCODE, but still relies on motif discovery algorithms to pinpoint the exact binding sites. In this thesis, the motif discovery problem is explored and a novel method based on weighted set cover is presented to identify the minimal set of motifs, with objective functions, that discriminately cover a set of DNA sequences. The results show that some motif set cover methods can more accurately identify biologically significant motifs over simply selecting the top scoring motifs. However, the weighed set cover algorithms did not perform exceptionally well when compared to standard selection methods, which is attributed to the use of a discriminative motif discovery application. Detailed results can be found at http://motifpipeline.com.
Lonnie Welch (Advisor)
David Juedes (Committee Member)
Sonsoles De Lacalle (Committee Member)
Frank Drews (Committee Member)
135 p.
Bioinformatics; Computer Science
Discriminative Motif Discovery; Weighted Set Cover; Greedy Set Cover; Linear Programming; ENCODE

Recommended Citations

Citations

  • Schmidt, R. J.M. (2015). Using Weighted Set Cover to Identify Biologically Significant Motifs [Master's thesis, Ohio University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1447797982

    APA Style (7th edition)

  • Schmidt, Robert. Using Weighted Set Cover to Identify Biologically Significant Motifs. 2015. Ohio University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1447797982.

    MLA Style (8th edition)

  • Schmidt, Robert. "Using Weighted Set Cover to Identify Biologically Significant Motifs." Master's thesis, Ohio University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1447797982

    Chicago Manual of Style (17th edition)

ohiou1447797982
745
© 2015, all rights reserved.
This open access ETD is published by Ohio University and OhioLINK.