The focus of this dissertation is the use of bioinformatics in the identification of highly conserved sequences among a set of poxvirus genomes and the subsequent functional analysis of the conserved functions of these sequences. A novel algorithm, Java Pattern Finder, which identifies sequences of a user-specified length that are conserved with a user-specified number of allowed differences, was used to identify near-perfectly conserved sequences among a set of poxvirus genomes. A scoring method was established to quantify the degree of conservation of these sequences and used to show that the 11 most conserved sequences were significantly more conserved than control sequences. Functional analysis showed that explanations such as low codon degeneracy or the presence of conserved promoter elements partially – but not fully – accounted for the conservation observed in these sequences, suggesting that these highly conserved regions may have novel functions in the poxvirus genome that have yet to be uncovered.
| Identifer | oai:union.ndltd.org:uvic.ca/oai:dspace.library.uvic.ca:1828/2027 |
| Date | 04 January 2010 |
| Creators | Sadeque, Aliya Mehreen |
| Contributors | Upton, Christopher |
| Source Sets | University of Victoria |
| Language | English, English |
| Detected Language | English |
| Type | Thesis |
| Rights | Available to the World Wide Web |
Page generated in 0.0018 seconds