基于DNA序列K-tuple分布的一种非序列比对分析

doi:10.3724/SP.J.1005.2010.00606

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HEREDITAS ›› 2010, Vol. 32 ›› Issue (6): 606-612.doi: 10.3724/SP.J.1005.2010.00606

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A new alignment-free sequence analysis based on the distribution of K-tuple

SHEN Juan¹, WU Wen-Wu², XIE Xiao-Li¹, GUO Man-Cai¹, YUAN Zhi-Fa¹

1. College of Science, Northwest A&F University, Yangling 712100, China;
2. College of Life Science, Northwest A&F University, Yangling 712100, China

Received:2009-09-15 Revised:2009-12-02 Online:2010-06-20 Published:2010-05-24
Contact: yuan zhifa E-mail:zhifayuan@nwsuaf.edu.cn

Abstract

Abstract:

Based on the distribution of K-tuple in complete genome, a method without doing sequence alignment to infer difference of biological sequence is proposed in this paper. The method can be used to measure the difference of distribution on K-tuple between the native DNA sequences and the corresponding randomized ones. Applied to construct phylogenetic trees of the complete mitochondrial genomes of 26 species of placental mammals, with K increasing, it yields phylogenetic trees of which the classification effect increasingly matches the result widely recognised by the biological field. The final results show that the phylogenetic trees built by this method is more reasonable than by other alignment-free sequence methods.

Key words: K-tuple, alignment-free sequence, DNA sequences, complete mitochondrial genomes, phylogenetic tree

CHEN Juan, TUN Wen-Wu, JIE Xiao-Chi, GUO Man-Cai, YUAN Zhi-Fa. A new alignment-free sequence analysis based on the distribution of K-tuple[J]. HEREDITAS, 2010, 32(6): 606-612.

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A new alignment-free sequence analysis based on the distribution of K-tuple

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