title: A combination dimensionality reduction approach to codon position patterns of eubacteria based on their complete genomes.
abstract: Graphical techniques have become powerful tools for the visualization and analysis of complicated biological systems. However, we cannot give such a graphical representation in a 2D/3D space when the dimensions of the represented data are more than three dimensions. The proposed method, a combination dimensionality reduction approach (CDR), consists of two parts: (i) principal component analysis (PCA) with a newly defined parameter ρ and (ii) locally linear embedding (LLE) with a proposed graphical selection for its optional parameter k. The CDR approach with ρ and k not only avoids loss of principal information, but also sufficiently well preserves the global high-dimensional structures in low-dimensional space such as 2D or 3D. The applications of the CDR on characteristic analysis at different codon positions in genome show that the method is a useful tool by which biologists could find useful biological knowledge.
authors.affiliation: College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, Hebei, People's Republic of China. zhqi_yh2004@yahoo.com.cn
authors.forename: Zhao-Hui
authors.initials: ZH
authors.lastname: Qi
authors.forename: Ruo-Yan
authors.initials: RY
authors.lastname: Wei
mesh_terms: D001419:Bacteria / Q000235:genetics*; D001482:Base Composition / Q000235:genetics; D003062:Codon / Q000235:genetics*; D030541:Databases, Genetic; D016680:Genome, Bacterial / Q000235:genetics*; D058011:Multifactor Dimensionality Reduction / Q000379:methods*; D009711:Nucleotides / Q000235:genetics; D025341:Principal Component Analysis; D012984:Software; D013211:Staphylococcus aureus / Q000235:genetics
chemical_list: D003062:Codon; D009711:Nucleotides