Constructing Phylogenetic Trees Based On The Mitochondrial Genome

Gene is the carrier of genetic information, describes the diverse forms of life.With the smooth completion of the human genome project and the rapiddevelopment of information technology, more and more complete genome sequencesare available for people to study, and this gives us the convenient conditions toexplain the mysteries of life from the perspective of gene biology. But in the processof reading the life "sealed book" which consists of only four words, the traditionalmethod of experimental observation seemed to be in difficulty, it must with the helpof mathematical principle and computer data processing algorithm to efficient andaccurate to analyze the biological sequence.In this paper, based on the traditional characteristic parameters of DNAsequence, a new characteristic parameters to describe the sequence information isput forward, it is Combination k-mer. As the distance, function Information entropyand discrete increment are used to construct for26kinds of placental mammals and64species of vertebrate, respectively. The full text is divided into four parts:In the first chapter, the development, the research status and significance ofphylogenetic tree, the application and development of the information entropy isintroduced, and the main work of this article is summed up briefly.The second chapter mainly describes the theory and method of this paper. Basedon the traditional characteristic parameters of DNA sequence, Combination k-mer isput forward as a new characteristic parameters to describe the sequence information;and the significance of Combination k-mer is proved through the analysis of the baserelevance; In this article, the distance function including new symmetric relativeentropy and discrete increment, based on the two kinds of distance function, thispaper use R software, through distance matrix method to construct the phylogenetictree.In the third chapter, analysis mitochondrial DNAand build the phylogenetic treefor26kinds of placental mammals and64species of vertebrate through the distancematrix. In this paper, three kinds of sequence characteristic parameters are used:6-mer, Combination6-mer and the combination of6-mer and Combination6-mer. When new symmetric relative entropy is used as distance function, distance matrixmethod and R software are used to constructs phylogenic trees for26kinds ofplacental mammals and64species of vertebrate. Calculation results show that, tojoin Combination6-mer in sequence characteristic parameters, especially when thedistant between the datatype string is57, can make the result more accurate then use6-mer solely; When increment of discrete is used as distance function, theeffectiveness is proved too; In addition, phylogenetic tree is more reasonable andcloser to the classification in biology when we chose new symmetric relative entropyas the distance function then discrete increment.