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Journal of Undergraduate Research

Keywords

probabilistic pair-hidden Markov model, SNP detection, sequencing data

College

Physical and Mathematical Sciences

Department

Computer Science

Abstract

In order to create and maintain a healthy human body, over three billion nucleotides (molecules of DNA, collectively called a genome) need to work together in harmony. Each cell in the human body needs its own copy of the genome, so during growth an individual’s DNA is replicated many times. Because the process of replication is not perfect, there are occasional mistakes. Sometimes, these mistakes can be fixed by the body’s own repair mechanisms, but occasionally, a single change in one of the three billion molecules in a human genome have lifethreatening results (for example, see the entry on Cystic Fibrosis at http://www.ncbi.nlm.nih.gov/omim/219700). In addition, certain changes (called Single Nucleotide Polymorphisms or SNPs, pronounced “snip”) that are passed on genetically do not have physical manifestations, but can cause a predisposition to a specific disease later in life. Much research over the past decade has been aimed toward first, identifying SNPs in different individuals, and then second, linking them with diseases.

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