Information Measure for Long-Range Correlated Sequences: the Case of the 24 Human Chromosomes

被引：24

作者：

Carbone, A. ^{[1
,2
,3
]}

机构：

[1] Politecn Torino, Turin, Italy

[2] Unita Univ Sapienza Roma, ISC CNR, Rome, Italy

[3] Swiss Fed Inst Technol, Zurich, Switzerland

来源：

SCIENTIFIC REPORTS | 2013年 / 3卷

关键词：

MAP; ENTROPY; DOMAINS; GENOME;

D O I：

10.1038/srep02721

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

A new approach to estimate the Shannon entropy of a long-range correlated sequence is proposed. The entropy is written as the sum of two terms corresponding respectively to power-law (ordered) and exponentially (disordered) distributed blocks (clusters). The approach is illustrated on the 24 human chromosome sequences by taking the nucleotide composition as the relevant information to be encoded/decoded. Interestingly, the nucleotide composition of the ordered clusters is found, on the average, comparable to the one of the whole analyzed sequence, while that of the disordered clusters fluctuates. From the information theory standpoint, this means that the power-law correlated clusters carry the same information of the whole analysed sequence. Furthermore, the fluctuations of the nucleotide composition of the disordered clusters are linked to relevant biological properties, such as segmental duplications and gene density.

引用

页数：10

共 31 条

[1] Applying Shannon's information theory to bacterial and phage genomes and metagenomes [J].

Akhter, Sajia ;

Bailey, Barbara A. ;

Salamon, Peter ;

Aziz, Ramy K. ;

Edwards, Robert A. .

SCIENTIFIC REPORTS, 2013, 3

[2] Recent segmental duplications in the human genome [J].

Bailey, JA ;

Gu, ZP ;

Clark, RA ;

Reinert, K ;

Samonte, RV ;

Schwartz, S ;

Adams, MD ;

Myers, EW ;

Li, PW ;

Eichler, EE .

SCIENCE, 2002, 297 (5583) :1003-1007

[3] Compositional segmentation and long-range fractal correlations in DNA sequences [J].

BernaolaGalvan, P ;

RomanRoldan, R ;

Oliver, JL .

PHYSICAL REVIEW E, 1996, 53 (05) :5181-5189

[4] The neoselectionist theory of genome evolution [J].

Bernardi, Giorgio .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (20) :8385-8390

[5] Alternate entropy measure for assessing volatility in financial markets [J].

Bose, Ranjan ;

Hamacher, Kay .

PHYSICAL REVIEW E, 2012, 86 (05)

[6] Alternate measure of information useful for DNA sequences [J].

Bose, Ranjan ;

Chouhan, Sonali .

PHYSICAL REVIEW E, 2011, 83 (05)

[7] Analysis of clusters formed by the moving average of a long-range correlated time series [J].

Carbone, A ;

Castelli, G ;

Stanley, HE .

PHYSICAL REVIEW E, 2004, 69 (02) :026105-1

[8] Scaling properties and entropy of long-range correlated time series [J].

Carbone, Anna ;

Stanley, H. Eugene .

PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 2007, 384 (01) :21-24

[9] Algorithm to estimate the Hurst exponent of high-dimensional fractals [J].

Carbone, Anna .

PHYSICAL REVIEW E, 2007, 76 (05)

[10] Standard deviations and correlations of GC levels in DNA sequences [J].

Clay, O .

GENE, 2001, 276 (1-2) :33-38

← 1 2 3 4 →