Assessment of genome visualization tools relevant to HIV genome research: development of a genome browser prototype

• Main Author: Boardman, Anelda Philine
• Other Authors: Hide, Winston
• Language: en
• Published: University of the Western Cape 2013
• Subjects: AIDS (Disease); Genetic aspects; HIV (Viruses); Data processing; Computer network resources; Genomics
• Online Access: http://hdl.handle.net/11394/2016

Magister Scientiae - MSc === Over the past two decades of HIV research, effective vaccine candidates have been elusive. Traditionally viral research has been characterized by a gene -by-gene approach, but in the light of the availability of complete genome sequences and the tractable size of the HIV genome, a genomic approach may improve insight into the biology and epidemiology of this virus. A genomic approach to finding HIV vaccine candidates can be facilitated by the use of genome sequence visualization. Genome browsers have been used extensively by various groups to shed light on the biology and evolution of several organisms including human, mouse, rat, Drosophila and C.elegans. Application of a genome browser to HIV genomes and related annotations can yield insight into forces that drive evolution, identify highly conserved regions as well as regions that yields a strong immune response in patients, and track mutations that appear over the course of infection. Access to graphical representations of such information is bound to support the search for effective HIV vaccine candidates. This study aimed to answer the question of whether a tool or application exists that can be modified to be used as a platform for development of an HIV visualization application and to assess the viability of such an implementation. Existing applications can only be assessed for their suitability as a basis for development of an HIV genome browser once a well-defined set of assessment criteria has been compiled. === South Africa