Phylogenetic Reconstruction Of viral Rna-dependent Rna Polymerases

Open Access
Author:
Ho, Ngai Lam
Graduate Program:
Computer Science and Engineering
Degree:
Master of Science
Document Type:
Master Thesis
Date of Defense:
May 25, 2012
Committee Members:
  • Piotr Berman, Thesis Advisor
Keywords:
  • RdRp PHYLOGENETIC RECONSTRUCTION OF VIRAL RNA-DEPENDENT RNA POLY
Abstract:
Viruses are found wherever there is life. Yet little is known how viruses evolved. Species of viruses evolve at a high mutation rate, making it hard to reconstruction their evolution accurately. Todate, no one has successfully classify the relationship of viral families and super-families. In this thesis I propose to reconstruct and study the evolutionary history of a common gene, or gene fragment of all Rna viruses: Rna dependent Rna polymerase or RdRp. I propose another algorithm to classify the catlytic regions of the RdRpsequences. By reconstructung the phylogenetic tree of RdRpcatalytic regions, the phylogenetic tree of the RdRp catlytic regions, it is shown that the constructed tree is highly accurately with viruses of families and super-families having common accestors. With the proposed algorithm and strategy of RdRp sequence collection. RdRp sequence can be collected, phylogenetic tree can be built with more monophyletic groups of viral families and super-families. It is hoped that the proposed phylogenetic tree of RdRp sequences can provide information for further information in viral research.