Electronic Theses and Dissertations

Identifier

1050

Date

2014

Date of Award

4-22-2014

Document Type

Thesis

Degree Name

Master of Science

Major

Bioinformatics

Committee Chair

Vinhthuy T Phan

Committee Member

Ramin Homayouni

Committee Member

Ebenezer O George

Abstract

Recent advances in biotechnology have enabled high-throughput sequencing of genomes based on large number of short reads. Current methods, however, depend mostly on aligning reads to only one reference genome at a time, making it difficult to differentiate sequencing errors from single nucleotide variants (SNV). We propose a method that attempts to take advantage of multiple genomes and SNV information to align reads. This approach is promising in that it allows us to distinguish between sequencing errors and SNV. Our proposed alignment algorithm uses read fragments to identify seeds, and extend these seeds to find occurrences of reads in genome. In this thesis, we have developed and implemented an algorithm using multiple genomes that captures genomic variations, indexes the multiple genomes and operates short read alignment on a collection of genomes. We also propose some possible ways of validating this work in the future.

Comments

Data is provided by the student.

Library Comment

dissertation or thesis originally submitted to the local University of Memphis Electronic Theses & dissertation (ETD) Repository.

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