Alignment-free comparison of genome sequences by a new numerical characterization |
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Authors: | Huang Guohua Zhou Houqing Li Yongfan Xu Lixin |
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Institution: | a Department of Mathematics, Shaoyang University, Shaoyang, Hunan 422000, China b Hunan First Normal College, Changsha, Hunan 410002, China |
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Abstract: | In order to compare different genome sequences, an alignment-free method has proposed. First, we presented a new graphical representation of DNA sequences without degeneracy, which is conducive to intuitive comparison of sequences. Then, a new numerical characterization based on the representation was introduced to quantitatively depict the intrinsic nature of genome sequences, and considered as a 10-dimensional vector in the mathematical space. Alignment-free comparison of sequences was performed by computing the distances between vectors of the corresponding numerical characterizations, which define the evolutionary relationship. Two data sets of DNA sequences were constructed to assess the performance on sequence comparison. The results illustrate well validity of the method. The new numerical characterization provides a powerful tool for genome comparison. |
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Keywords: | Alignment-free comparison Graphical representation DNA sequence Numerical characterization Phylogenetic tree |
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