Full Text Available
Note: Clicking the button above will open the full text document at the original institutional repository in a new window.
New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms
Thesis (PhD)--University of Pretoria, 2010.
Saved in:
| Other Authors: | |
|---|---|
| Format: | Thesis |
| Published: |
University of Pretoria
2013
|
| Subjects: | |
| Tags: |
No Tags, Be the first to tag this record!
|
| _version_ | 1867613580066553856 |
|---|---|
| access_status_str | Open Access |
| author2 | Reva, Oleg N. |
| author_browse | Reva, Oleg N. |
| author_facet | Reva, Oleg N. |
| collection | Thesis |
| dc_rights_str_mv | © 2009, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
| description | Thesis (PhD)--University of Pretoria, 2010. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/25245 |
| institution | University of Pretoria (South Africa) |
| last_indexed | 2026-06-10T12:38:24.243Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2013 |
| publishDateRange | 2013 |
| publishDateSort | 2013 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/25245 New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms Reva, Oleg N. Joubert, Fourie ham.kzn@gmail.com Ganesan, Hamilton Nucleotide polymorphisms Comparative genomics UCTD Thesis (PhD)--University of Pretoria, 2010. Tuberculosis is one of the leading causes of mortality globally. Although this disease has been around for many generations, treatment and management of the disease remains a daunting challenge. M. tb, is one of the most famous tuberculosis causing organisms, however there are many other mycobacterial strains and species that are also responsible for human mortality, globally. Not all mycobacterial species, however, are disease causing. It is only a few strains such as M. tb H37Rv, M. tb CDC1551, M. tb F11 and M. bovis which are responsible for causing disease. The rest are relatively harmless. What are the genetic differences between these virulent and avirulent strains that dictate a strain's behavior? The answers to these and many other questions lie hidden within the genomes of these organisms. Due to the great advances in DNA sequencing techniques, it is now now possible to more quickly and cheaply, sequence whole bacterial genomes in a single experimental run (High-throughput sequencing). Comparative genomics is therefore extremely relevant and important to be able to handle the dubious amounts of genomic data being poured into our public databases. Several comparative genomics environments already exist on the web today, however the goal of this project is to produce a web-based, comparative genomics environment which not only incorporates basic comparative genomics functions but also, novel tools such as the Seqword Genome Browser (SWGB) and the Mycobacterial Comparison Project (MCP). Using these tools, some interesting comparative genomics findings regarding certain strains of Mycobacteria are made. We reveal several genomic islands within M. avium and M. tb H37Rv. It is shown that certain genes which are usually found to be conserved among other bacteria, tend to be rather divergent among the mycobacteria. 'Mutational hotspots' containing many DNA replication genes are observed to have higher mutation rates relative to the rest of the genome which perhaps accounts for the slow-growth rate of these bacteria. By looking at the genetic profile of PE-PGRS genes in mycobacteria it was shown that M. tb H37Rv and M. tb F11 were actually closer for several genes than when compared to strain H37Ra. The finding was unexpected as H37Ra is known to be derived from H37Rv. These findings are extremely important in the area of TB research as it is of extreme importance to be able to trace areas of greater or lower selection within mycobacteria. Automated sequence comparison such as this is also important for tracking drug resistance markers and other features within mycobacteria so that more focused research can be carried out. The built system was tested and validated with mycobacteria, however, the system is flexible and designed with the intent of inclusion of any prokaryotic organism. It is hoped that systems such as these, and other advances in sequence comparison technology in the future, will provide the understanding needed to better control and cure diseases in the future. Biochemistry unrestricted 2013-09-06T20:03:16Z 2010-06-07 2013-09-06T20:03:16Z 2010-04-28 2010-06-07 2010-06-04 Thesis Ganesan, H 2009, New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd < http://hdl.handle.net/2263/25245 > D10/394/ag http://hdl.handle.net/2263/25245 http://upetd.up.ac.za/thesis/available/etd-06042010-004142/ © 2009, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. application/pdf application/pdf application/pdf application/pdf application/pdf application/pdf application/pdf application/pdf University of Pretoria |
| spellingShingle | Nucleotide polymorphisms Comparative genomics UCTD New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms |
| title | New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms |
| title_full | New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms |
| title_fullStr | New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms |
| title_full_unstemmed | New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms |
| title_short | New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms |
| title_sort | new tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms |
| topic | Nucleotide polymorphisms Comparative genomics UCTD |
| url | http://hdl.handle.net/2263/25245 http://upetd.up.ac.za/thesis/available/etd-06042010-004142/ |