Study of DNA binding sites using the Renyi parametric entropy measure

Krishnamachari A; Mandal VM; Karmeshu

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Study of DNA binding sites using the Renyi parametric entropy measure

机译：使用Renyi参数熵测度研究DNA结合位点

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Shannon's definition of uncertainty or surprisal has been applied extensively to measure the information content of aligned DNA sequences and characterizing DNA binding sites. In contrast to Shannon's uncertainty, this study investigates the applicability and suitability of a parametric uncertainty measure due to Renyi. It is observed that this measure also provides results in agreement with Shannon's measure, pointing to its utility in analysing DNA binding site region. For facilitating the comparison between these uncertainty measures. a dimensionless quantity called "redundancy" has been employed. It is found that Renyi's measure at low parameter values possess a better delineating feature of binding sites (of binding regions) than Shannon's measure. The critical value of the parameter is chosen with an outlier criterion. (C) 2003 Elsevier Ltd. All rights reserved.

机译：Shannon对不确定性或意外发生的定义已广泛用于测量对齐的DNA序列的信息含量和表征DNA结合位点。与Shannon的不确定性相反，本研究调查了由于Renyi引起的参数不确定性度量的适用性和适用性。观察到，该措施也提供了与香农的措施一致的结果，指出了其在分析DNA结合位点区域中的用途。为了促进这些不确定性措施之间的比较。已经使用了称为“冗余”的无量纲数量。发现在低参数值下的人意测度具有比香农测度更好的（结合区域的）结合位点的描绘特征。参数的临界值是根据异常标准选择的。（C）2003 Elsevier Ltd.保留所有权利。

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《Journal of Theoretical Biology》 |2004年第3期|共8页
作者
Krishnamachari A; Mandal VM; Karmeshu;
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正文语种 eng
中图分类普通生物学;
关键词
Shannon entropy; Renyi entropy; information theory; DNA binding sites; uncertainty measures; NUCLEOTIDE-SEQUENCES; INFORMATION-CONTENT; NUCLEIC-ACIDS;

机译：Shannon熵;Renyi熵;信息论;DNA结合位点;不确定性测度;核苷酸序列;信息含量;核酸;

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1. Study of DNA binding sites using the Renyi parametric entropy measure [J] . Krishnamachari A, Mandal VM, Karmeshu Journal of Theoretical Biology . 2004,第3期

机译：使用Renyi参数熵测度研究DNA结合位点
2. How Does a DNA Interacting Enzyme Change Its Specificity during Molecular Evolution? A Site-Directed Mutagenesis Study at the DNA Binding Site of the DNA-(Adenine-N~6)-methyltransferase EcoRV [J] . Carsten Beck, Susanne Cranz, Merdol Solmaz, Biochemistry . 2001,第37期

机译：DNA相互作用酶在分子进化过程中如何改变其特异性？在DNA-（腺嘌呤-N〜6）-甲基转移酶EcoRV的DNA结合位点进行定点诱变研究
3. A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery. [J] . Wang Xiaohu, Gao Haichun, Shen Yufeng, Nucleic Acids Research . 2008,第15期

机译：一种高通量的结合百分比策略，用于测量DNA-蛋白质相互作用中的结合能：在基因组规模位点发现中的应用。
4. DNA Binding Sites Characterization by Means of Renyi Entropy Measures on Nucleotide Transitions [C] . Alexandre Perera, Montserrat Vallverdu, Francesc Claria, Annual International Conference of the IEEE Engineering in Medicine and Biology Society . 2006

机译：DNA结合位点通过尼西熵措施对核苷酸过渡的熵措施表征
5. Computing conditional probabilities in large domains by maximizing Renyi's quadratic entropy. [D] . Zitnick, Charles Lawrence, III. 2003

机译：通过最大化Renyi的二次熵来计算大范围内的条件概率。
6. The lambda terminase enzyme measures the point of its endonucleolytic attack 47 +/- 2 bp away from its site of specific DNA binding the R site. [O] . R R Higgins, A Becker 1994

机译：λ末端酶测量距离其特异性DNA结合位点R位点47 +/- 2 bp的核酸内切攻击点。
7. A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery [O] . Wang, Xiaohu, Gao, Haichun, Shen, Yufeng, 2008

机译：一种高通量结合百分比策略，用于测量DNA与蛋白质相互作用中的结合能：在基因组规模的位点发现中的应用
8. DNA Binding Drugs Targeting the Regulatory DNA Binding Site of the ETS Domain Family Transcription Factor Associated with Human Breast Cancer [R] . Wang, Y. 2001

机译：靶向与人乳腺癌相关的ETs结构域家族转录因子的调节DNa结合位点的DNa结合药物

Study of DNA binding sites using the Renyi parametric entropy measure

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