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Repeat Sequences and Base Correlations in Human Y ChromosomePalindromes
Neng-zhi Jin,Zi-xian Liu,Yan-jiao Qi,Wen-yuan Qiu*
Author NameAffiliationE-mail
Neng-zhi Jin Department of Chemistry, State Key Laboratory of Applied Organic Chemistry, Lanzhou University,Lanzhou 730000, China  
Zi-xian Liu Department of Chemistry, State Key Laboratory of Applied Organic Chemistry, Lanzhou University,Lanzhou 730000, China  
Yan-jiao Qi Department of Chemistry, State Key Laboratory of Applied Organic Chemistry, Lanzhou University,Lanzhou 730000, China  
Wen-yuan Qiu* Department of Chemistry, State Key Laboratory of Applied Organic Chemistry, Lanzhou University,Lanzhou 730000, China wyqiu@lzu.edu.cn 
Abstract:
On the basis of information theory and statistical methods, we use mutual information, n-tuple entropy and conditional entropy, combined with biological characteristics, to analyze the long range correlation and short range correlation in human Y chromosome palindromes.The magnitude distribution of the long range correlation which can be reflected by the mutual information is P5>P5a>P5b (P5a and P5b are the sequences that replace solely Alu repeats and all interspersed repeats with random uncorrelated sequences in human Y chromosome palindrome 5, respectively); and the magnitude distribution of the short range correlation which can be reflected by the n-tuple entropy and the conditional entropy is P5>P5a>P5b>random uncorrelated sequence. In other words, when the Alu repeats and all interspersed repeats replace with random uncorrelated sequence, the long range and short range correlation decrease gradually. However, the random uncorrelated sequence has no correlation. This research indicates that more repeat sequences result in stronger correlation between bases in human Y chromosome. The analyses may be helpful to understand the special structures of human Y chromosome palindromes profoundly.
Key words:  Human Y chromosome, Palindrome, Mutual information, Long range correlation, Short range correlation
FundProject:
Repeat Sequences and Base Correlations in Human Y ChromosomePalindromes
金能智,刘子贤,齐燕姣,邱文元*
摘要:
利用信息论和统计学的方法并结合生物学的特征研究人类Y染色体回文序列的互信息、“n字”熵、条件熵,定量分析了回文序列的长程关联和短程关联,发现其中既存在长程关联也存在短程关联,并且它们主要是由序列中的重复序列引起的. 研究表明重复序列含量越高碱基之间的关联越强.
关键词:  人类Y染色体,回文序列,互信息,长程关联,短程关联
DOI:10.1088/1674-0068/22/03/255-261
分类号: