Dissertation > Excellent graduate degree dissertation topics show

Phylogenetic Tree Construction Based on Hierarchical Clustering

Author: LiaoLiJiao
Tutor: LiaoBo
School: Hunan University
Course: Computer Science and Technology
Keywords: constructing phylogentic trees hierarchical clustering distance matrix self-organizing map
CLC: TP301.6
Type: Master's thesis
Year: 2011
Downloads: 77
Quote: 1
Read: Download Dissertation

Abstract


Molecular phylogenetic analysis is one of the most important fields inbioinformatics, which mainly studies homologous DNA or protein sequences and theevolution analysis for protein sequences or DNA sequences. So the phylogenetic treeis obtained which is reflected evolutionary relationship of protein sequences or DNAsequences. The research of phylogenetic tree reconstruction has a long time history; itplays a more and more important part in molecular evolution and phylogeneticresearch. The phylogenetic tree reflects the sequence of the species evolution, it helpsus to find the history and evolution mechanism of species. Phylogenetic treeconstruction methods can be obtained different categories of the different views, sowe can divide the phylogenetic tree construction methods into two categories: basedon mathematics clustering method and based on the optimal search method. As basedon optimal search methods are much slower than based on mathematics clusteingmethods, based on mathematics clustering method has wide applications.The hierarchical clustering method of based on mathematics clustering method isa generally method in phylogenetic trees construction, but the traditional mathematicsclustering method is built to base on sequence alignment. Therefore, in order to solvethis problem, we propose two new methods based on the hierarchical clustering, bothof which are without sequence alignment, and relatively intuitive, less calculation,easy to understand. These methods are the vertical and horizontal method and basedon changed weight by self-organizing map method.The vertical and horizontal method is also based on distance matrix method. It isbased on the distance matrix, and finds some points in these horizontal and someedges in these vertical to get a binary tree, and then we implemente clustering.Based on changed weight by self-organizing map method is proposed for basingon self-organizing map network. Self-organizing map network can be applied to bothclassification and clustering, and also be used in phylogenetic analysis andevolutionary tree construction. But when the self-organizing map network is usedphylogenetic analysis and evolutionary tree construction, the algorithm is complex, sowe propose this method which reduces the complexity of the algorithm. It is comparedwith based on distance matrix method, which should not be similar analysis toconstruct the distance matrix, and directly get a minimum weight tree. Finally weconstruct the phylogenetic tree by clustering. In order to assess the method feasibility of constructing the phylogenetic trees,we often use Neighbor.exe program of PHYLIP software to assess, we verify themethod feasibility by the experiment.

Related Dissertations

  1. An Improvement of Cluster on Phylogenetic Profiling Method,TP311.13
  2. Based on the User’s Perceptual Needs’ Handle GPS Design,TN967.1
  3. Web-based social network search method to judge the identity of names,TP393.09
  4. Packet-based network key nodes dynamic weighting algorithm,TP393.09
  5. Membrane protein transmembrane helix prediction,Q51
  6. Kernel-based SOM time series prediction,O211.61
  7. A Manifold Learning-Based Multi-Objective Estimation of Distribution Algorithm,TP301.6
  8. Reactive Power Optimization Based on Hierarchical Clustering and Ant Colony Optimization Algorithm,TM714.3
  9. Loading Optimization Method Based on Two Level Clustering,U492.22
  10. Research on Data Acquisition and Topic Analysis of Online Public Opinion,TP393.09
  11. Internet News Hot Mining System Research and Implementation,TP393.09
  12. Research and Application of Network Consensus Guidance System Using Community Detection,TP393.09
  13. A New Hierarchical Clustering Algorithm Study and Application,TP311.13
  14. The Topological Network and Investing Roadmap Strategies of China’s A-share Market,F224
  15. Structure Learning Algorithm Based Bayesian Network,TP311.13
  16. Based on pseudo- amino acid composition of the protein sequence classification,Q51
  17. The Formation Control and Cooperation Research of Robot Based on MAS,TP242
  18. Research of Face Recognition Based on Algebraic Feature and DSP Implementation,TP391.41
  19. The Improvement of Genetic Algorithm and It’s Application on Knapsack Problem,TP18
  20. Multi-class Fuzzy Support Vector Machine Based on Dismissing Margin,O212
  21. The Characteristics of the Arch Form of Skeletal Class Ⅲ Occlusion with Normal Maxilla and Protruding Mandible,R783.5

CLC: > Industrial Technology > Automation technology,computer technology > Computing technology,computer technology > General issues > Theories, methods > Algorithm Theory
© 2012 www.DissertationTopic.Net  Mobile