Phylogenetic analysis of Klebsiella pneumoniae genomes
Date Issued
2016
Date
2016
Author(s)
Wang, Liang-Jhih
Abstract
In Taiwan, Klebsiella pneumonia is prominent in people who have diabetes and causes complications including pneumonia, sepsis, liver abscess, etc. Capsular is the main etiological factor. Also, capsular polysaccharide belongs to water-soluble and meta-acidic and its compositions are found to have highly variability. In this thesis, we want to find out in which algorithms the local optimal phylogentic tree is constructed by comparing ten strains of Klebsiella pneumonia of capsular polysaccharides, including NTUH-2044、K1、K2、K5、K9、K14、K52、NK8、NK29、NK245, observing similarities of genes among ten strains, constructing phylogenetic trees by various algorithms and then using the Robinson-foulds distance. According to the result of comparative sequence analysis overview, sequences in galf, wzi, gnd and ugd regions have higher similarities. However, the similarity in cps without 5'' and 3'' is low in general but in wzc and wcal region are higher. When calculating the distance of phylogenetic trees, the RF distance is relatively low under the situation of maximum parsimony method with whole cps and without 5'' and 3''; therefore, the phylogenetic trees constructed by them are the local optimal phylogenetic tree among three algorithms.
Subjects
Klebsiella pneumonia
phylogenetic tree
multiple sequencealignments
Neighbor-joining
Maximum parsimony
Maximum-likelihood
Robinson-foulds distance
SDGs
Type
thesis