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Publication Date

Spring 2010

Degree Type

Thesis - Campus Access Only

Degree Name

Master of Science (MS)

Department

General Engineering

Advisor

Sami Khuri

Keywords

hemoglobin, phylogenetic tree, sequence alignment, sickle cell anemia, Single Nucleotide Polymorphism, SNP

Subject Areas

Biology; Bioinformatics

Abstract

The term single nucleotide polymorphism (SNP) refers to the occurrence of small,

i.e., single nucleotide, change in the DNA sequence of an organism. Many common and

significant diseases like Alzheimer's and diabetes have been attributed to the presence of

SNPs in the human genome. This thesis investigates new and simpler methods to reliably

identify malicious SNPs related to a particular disease in the human genome. We have

developed a system called the RIADS-SNP Analyzer to identify and isolate harmful dis-

ease causing SNPs based on the affected amino acid, their biochemical properties, and

consequent change in protein structure. The RIADS system has three main components:

learning component, testing component, and annotation component. All three compo-

nents have been implemented and the results have been verified with existing packages

using the hemoglobin gene sequence as a case study.

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