Masters Theses

Date of Award

12-1994

Degree Type

Thesis

Degree Name

Master of Science

Major

Biomedical Engineering

Major Professor

Richard J. Mural

Committee Members

Lisa Stubbs, Frank Larimer

Abstract

CpG islands are short regions within mammalian DNA having a high G+C content and a nonsuppressed CpG dinucleotide frequency. Since all known CpG islands are located either within a gene or within close proximity to one, their presence is a landmark for a large number of genes within the genome. This aspect can be exploited by researchers characterizing and mapping the genome. Whereas most documented CpG islands are associated with the 5' regions of genes, a significant fraction are located downstream of the transcription initiation site. Whether the association of CpG islands with genes is fortuitous is not known; however, the information supplied by their presence in a sequence can be applied without this knowledge. The purpose of this work was to develop a computational means for distinguishing a CpG island located within the 5' region of a human gene from one located within the 3' body of a transcript based on its DNA sequence. This distinction would be valuable in extracting the maximum amount of information from either a genomic clone or an anonymous DNA sequence. The resulting CpG classifier was developed using a word preference based method and correctly distinguished 90.7% of a test set consisting of approximately one- third of all known human CpG islands. This tool should be useful for biologists for designing experiments and may provide insights into the function and derivation of the CpG islands.

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