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MAPPING TRILLIONS OF SHORT DNA READS TO A REFERENCE
GENOME AND ITS APPLICATIONS
by
Yang-Ho Chen
A Dissertation Presented to the
FACULTY OF THE USC GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Ful llment of the
Requirements for the Degree
DOCTOR OF PHILOSOPHY
(COMPUTATIONAL BIOLOGY AND BIOINFORMATICS)
December 2011
Copyright 2011 Yang-Ho Chen
Object Description
| Title | Mapping trillions of short DNA reads to a reference genome and its applications |
| Author | Chen, Yang-Ho |
| Author email | yanghoch@usc.edu;chen.yangho@gmail.com |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Computational Biology and Bioinformatics |
| School | College of Letters, Arts And Sciences |
| Date defended/completed | 2011-10-20 |
| Date submitted | 2011-11-01 |
| Date approved | 2011-11-02 |
| Restricted until | 2011-11-02 |
| Date published | 2011-11-02 |
| Advisor (committee chair) | Chen, Ting |
| Advisor (committee member) |
Smith, Andrew D Kempe, David |
| Abstract | The breakthrough of second-generation sequencing has opened the door for many applications. In these applications, mapping massive amounts of short DNA reads to a reference sequence is a key step. This thesis proposes novel periodic seed algorithms to perform the mapping tasks. New seed design algorithms are also proposed for various mapping criteria. Compared with other read mapping algorithms, the proposed algorithms better balance speed, memory usage, and various sequencing platforms under reasonable settings. The algorithm is implemented as two short read aligners: PerM and Clippers. PerM is capable of performing rapid general-purpose un-gapped alignments for Illumina and SOLiD reads. Clippers is designed to align 75-bp or longer Illumina reads with one gap and multiple mismatches. The discovery of alignments with a long gap is integral for two tasks: finding splicing events in gene expression and locating structural variations in genomes. |
| Keyword | short read mapping; NGS; illumina; SOLiD; PerM; second generation sequencing; alignments; |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m |
| Rights | Chen, Yang-Ho |
| Access conditions | The author retains rights to his/her dissertation, thesis or other graduate work according to U.S. copyright law. Electronic access is being provided by the USC Libraries in agreement with the author, as the original true and official version of the work, but does not grant the reader permission to use the work if the desired use is covered by copyright. It is the author, as rights holder, who must provide use permission if such use is covered by copyright. The original signature page accompanying the original submission of the work to the USC Libraries is retained by the USC Libraries and a copy of it may be obtained by authorized requesters contacting the repository e-mail address given. |
| Repository name | University of Southern California Digital Library |
| Repository address | USC Digital Library, University of Southern California, University Park Campus MC 7002, 106 University Village, Los Angeles, California 90089-7002, USA |
| Repository email | cisadmin@usc.edu |
| Archival file | uscthesesreloadpub_Volume71/etd-ChenYangHo-383.pdf |
Description
| Title | Page 1 |
| Full text | MAPPING TRILLIONS OF SHORT DNA READS TO A REFERENCE GENOME AND ITS APPLICATIONS by Yang-Ho Chen A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Ful llment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (COMPUTATIONAL BIOLOGY AND BIOINFORMATICS) December 2011 Copyright 2011 Yang-Ho Chen |
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