Neng-zhi Jin, Zi-xian Liu, Yan-jiao Qi, Wen-yuan Qiu. Repeat Sequences and Base Correlations in Human Y ChromosomePalindromes[J]. Chinese Journal of Chemical Physics , 2009, 22(3): 255-261. doi: 10.1088/1674-0068/22/03/255-261
Citation: Neng-zhi Jin, Zi-xian Liu, Yan-jiao Qi, Wen-yuan Qiu. Repeat Sequences and Base Correlations in Human Y ChromosomePalindromes[J]. Chinese Journal of Chemical Physics , 2009, 22(3): 255-261. doi: 10.1088/1674-0068/22/03/255-261

Repeat Sequences and Base Correlations in Human Y ChromosomePalindromes

doi: 10.1088/1674-0068/22/03/255-261
Funds:  This work was supported by the National Natural Science Foundation of China (No.20173023 andNo.90203012) and the Specialized Research Fund for the Doctoral Program of Higher Education of China(No.20020730006).
  • Received Date: 2008-12-28
  • 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.
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    沈阳化工大学材料科学与工程学院 沈阳 110142

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Repeat Sequences and Base Correlations in Human Y ChromosomePalindromes

doi: 10.1088/1674-0068/22/03/255-261
Funds:  This work was supported by the National Natural Science Foundation of China (No.20173023 andNo.90203012) and the Specialized Research Fund for the Doctoral Program of Higher Education of China(No.20020730006).

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.

Neng-zhi Jin, Zi-xian Liu, Yan-jiao Qi, Wen-yuan Qiu. Repeat Sequences and Base Correlations in Human Y ChromosomePalindromes[J]. Chinese Journal of Chemical Physics , 2009, 22(3): 255-261. doi: 10.1088/1674-0068/22/03/255-261
Citation: Neng-zhi Jin, Zi-xian Liu, Yan-jiao Qi, Wen-yuan Qiu. Repeat Sequences and Base Correlations in Human Y ChromosomePalindromes[J]. Chinese Journal of Chemical Physics , 2009, 22(3): 255-261. doi: 10.1088/1674-0068/22/03/255-261

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