弦的实际频率与预期频率的比较揭示了大分子的信息容量。
Comparison of Real Frequencies of Strings vs. the Expected Ones Reveals the Information Capacity of Macromoleculae.
作者信息
Sadovsky Michael G
机构信息
Division of Russian Academy of Sciences, Institute of Biophysics of Siberian, Akademgorodok, Krasnoyarsk, 660036.
出版信息
J Biol Phys. 2003 Mar;29(1):23-38. doi: 10.1023/A:1022554613105.
Abstract
The information capacity of nucleotide sequences is defined through the calculation of specific entropy of their frequency dictionary. The specificentropy of the frequency dictionary is calculated against the reconstructeddictionary; this latter bears the most probable continuations of the shorterstrings. This developed measure allows to distinguish the sequences both from the randons ones, and from those with high level of (rather simple) order. Some implications of the developed methodology in the fields of genetics,bioinformatics, and molecular biology are discussed.
摘要
核苷酸序列的信息容量是通过计算其频率字典的比熵来定义的。频率字典的比熵是相对于重建字典计算的；后者包含较短字符串最可能的延续。这种改进的度量方法能够区分随机序列和具有高度（相当简单）有序性的序列。本文还讨论了这种改进方法在遗传学、生物信息学和分子生物学领域的一些应用。
相似文献
1
Comparison of Real Frequencies of Strings vs. the Expected Ones Reveals the Information Capacity of Macromoleculae.弦的实际频率与预期频率的比较揭示了大分子的信息容量。
J Biol Phys. 2003 Mar;29(1):23-38. doi: 10.1023/A:1022554613105.
2
Information capacity of nucleotide sequences and its applications.
Bull Math Biol. 2006 May;68(4):785-806. doi: 10.1007/s11538-005-9017-0. Epub 2006 Apr 7.
3
Genes, information and sense: complexity and knowledge retrieval.基因、信息与意义：复杂性与知识检索
Theory Biosci. 2008 Jun;127(2):69-78. doi: 10.1007/s12064-008-0032-1. Epub 2008 Apr 29.
4
The method to compare nucleotide sequences based on the minimum entropy principle.
Bull Math Biol. 2003 Mar;65(2):309-22. doi: 10.1016/S0092-8240(02)00107-6.
5
[Information capacity of the nucleotide sequences and their fragments].
Biofizika. 1997 Sep-Oct;42(5):1047-53.
6
High-recall protein entity recognition using a dictionary.使用词典进行高召回率蛋白质实体识别。
Bioinformatics. 2005 Jun;21 Suppl 1(Suppl 1):i266-73. doi: 10.1093/bioinformatics/bti1006.
7
Entropy and complexity of finite sequences as fluctuating quantities.作为波动量的有限序列的熵与复杂性。
Biosystems. 2002 Jan;64(1-3):23-32. doi: 10.1016/s0303-2647(01)00171-x.
8
[Classification of nucleotide sequences over their frequency dictionaries reveals a relation between the structure of sequences and taxonomy of their bearers].
Zh Obshch Biol. 2003 Jan-Feb;64(1):65-77.
9
Nonlinear analysis of tRNAs nucleotide sequences by random walks: randomness and order in the primitive informational polymers.通过随机游走对转运RNA核苷酸序列进行非线性分析：原始信息聚合物中的随机性与有序性
J Mol Evol. 2015 Feb;80(2):81-5. doi: 10.1007/s00239-015-9664-1. Epub 2015 Jan 11.
10
[A correlational approach to the comparison of nucleotide sequences].
Zh Obshch Biol. 1994 Jul-Oct;55(4-5):420-30.
引用本文的文献
1
Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer.基于无比对方法的病毒系统发生基因组学：确定 k-mer 最优长度的三步法。
Sci Rep. 2017 Jan 19;7:40712. doi: 10.1038/srep40712.
2
Self-organization and entropy reduction in a living cell.活细胞中的自组织与熵减
Biosystems. 2013 Jan;111(1):1-10. doi: 10.1016/j.biosystems.2012.10.005. Epub 2012 Nov 15.
3
Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution.原核生物全蛋白质组系统发育的特征频率分布：一种具有最优特征分辨率的无比对方法。
Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):133-8. doi: 10.1073/pnas.0913033107. Epub 2009 Dec 14.
4
Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method.采用无比对方法对大型双链DNA病毒家族进行全蛋白质组系统发育分析。
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12826-31. doi: 10.1073/pnas.0905115106. Epub 2009 Jun 24.
5
Genes, information and sense: complexity and knowledge retrieval.基因、信息与意义：复杂性与知识检索
Theory Biosci. 2008 Jun;127(2):69-78. doi: 10.1007/s12064-008-0032-1. Epub 2008 Apr 29.
本文引用的文献
1
Entropy and complexity of finite sequences as fluctuating quantities.作为波动量的有限序列的熵与复杂性。
Biosystems. 2002 Jan;64(1-3):23-32. doi: 10.1016/s0303-2647(01)00171-x.
2
Correlation property of length sequences based on global structure of the complete genome.基于完整基因组全局结构的长度序列的相关性特性。
Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Jan;63(1 Pt 1):011903. doi: 10.1103/PhysRevE.63.011903. Epub 2000 Dec 20.
3
Information content of protein sequences.蛋白质序列的信息内容。
J Theor Biol. 2000 Oct 7;206(3):379-86. doi: 10.1006/jtbi.2000.2138.
4
Evolution of biological information.生物信息的进化
Nucleic Acids Res. 2000 Jul 15;28(14):2794-9. doi: 10.1093/nar/28.14.2794.
5
[Evaluation of genetic test redundancy using a high-frequency component of the l-gram graph].[使用l-gram图的高频分量评估基因检测冗余性]
Biofizika. 1999 Jul-Aug;44(4):639-48.
6
Zones of low entropy in genomic sequences.基因组序列中的低熵区域。
Comput Chem. 1999 Jun 15;23(3-4):275-82. doi: 10.1016/s0097-8485(99)00009-1.
7
Significantly lower entropy estimates for natural DNA sequences.天然DNA序列的熵估计值显著更低。
J Comput Biol. 1999 Spring;6(1):125-42. doi: 10.1089/cmb.1999.6.125.
8
On the informational content of overlapping genes in prokaryotic and eukaryotic viruses.关于原核生物和真核生物病毒中重叠基因的信息内容。
J Mol Evol. 1997 Jun;44(6):625-31. doi: 10.1007/pl00006185.
9
[Determination of the amount of information in nucleotide sequences].
Mol Biol (Mosk). 1996 May-Jun;30(3):529-41.
10
[Introns differ from exons by their redundancy].内含子与外显子的不同之处在于其冗余性。
Genetika. 1995 Oct;31(10):1365-9.
Zotero 插件