Journal of South China University of Technology(Natural Science Edition) ›› 2012, Vol. 40 ›› Issue (8): 106-109.

• Biological Engineering • Previous Articles     Next Articles

Local Alignment-Free Sequences Based on D2shepp Statistics

Liu Xue-mei  Wen De-hua  Yu Huang-zhong  Gao Ya-ni   

  1. Department of Physics,South China University of Technology,Guangzhou 510640,Guangdong,China
  • Received:2011-03-18 Revised:2011-11-28 Online:2012-08-25 Published:2012-07-01
  • Contact: 刘雪梅(1975-) ，女，博士，讲师，主要从事生物物理研究． E-mail:liuxm@ scut.edu.cn
  • About author:刘雪梅(1975-) ，女，博士，讲师，主要从事生物物理研究．
  • Supported by:

    国家自然科学基金资助项目( 10947023， 61176061) ; 华南理工大学中央高校基本科研业务费专项资金资助项目( 20112M0088)

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Abstract:

The similarities between two biological sequences is a major issue in computational biology,and a fast D2shepp statistics method based on the joint k-tuple content in two sequences has been used in the alignment-free sequence comparison. In this paper,two separate random sequences are generated based on the zero model,and their local alignment is conducted based on D2shepp statistics,thus obtaining the optimal values and the sum of these values. Then,the Power distribution is simulated and the distributions with different k values are analyzed. Finally,with the same parameters,the proposed local alignment is compared with the global alignment based on D2shepp statistics. It is found that the Power value of the proposed local alignment rapidly approaches 1 with the increase of the sequence length and that the proposed local alignment is quicker and more accurate than the global one.

Key words: alignment-free sequence, D2shepp statistics, local alignment, Power value