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Open Access Highly Accessed Research article

The human genome: a multifractal analysis

Pedro A Moreno1*, Patricia E Vélez23, Ember Martínez4, Luis E Garreta1, Néstor Díaz4, Siler Amador4, Irene Tischer1, José M Gutiérrez5, Ashwinikumar K Naik6, Fabián Tobar3 and Felipe García3

Author affiliations

1 Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Santiago de Cali, Colombia

2 Profesora del Departamento de Biología, FACNED, Universidad del Cauca, Popayán, Colombia

3 Escuela de Ciencias Básicas. Facultad de Salud, Universidad del Valle, Santiago de Cali, Colombia

4 Departamento de Sistemas, Universidad del Cauca, Popayán, Colombia

5 Instituto de Física de Cantabria, Universidad de Cantabria-CSIC, Santander, España

6 Vaatsalya HealthCare Solutions Pvt Ltd, Bangalore, India

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Citation and License

BMC Genomics 2011, 12:506  doi:10.1186/1471-2164-12-506

Published: 14 October 2011

Abstract

Background

Several studies have shown that genomes can be studied via a multifractal formalism. Recently, we used a multifractal approach to study the genetic information content of the Caenorhabditis elegans genome. Here we investigate the possibility that the human genome shows a similar behavior to that observed in the nematode.

Results

We report here multifractality in the human genome sequence. This behavior correlates strongly on the presence of Alu elements and to a lesser extent on CpG islands and (G+C) content. In contrast, no or low relationship was found for LINE, MIR, MER, LTRs elements and DNA regions poor in genetic information. Gene function, cluster of orthologous genes, metabolic pathways, and exons tended to increase their frequencies with ranges of multifractality and large gene families were located in genomic regions with varied multifractality. Additionally, a multifractal map and classification for human chromosomes are proposed.

Conclusions

Based on these findings, we propose a descriptive non-linear model for the structure of the human genome, with some biological implications. This model reveals 1) a multifractal regionalization where many regions coexist that are far from equilibrium and 2) this non-linear organization has significant molecular and medical genetic implications for understanding the role of Alu elements in genome stability and structure of the human genome. Given the role of Alu sequences in gene regulation, genetic diseases, human genetic diversity, adaptation and phylogenetic analyses, these quantifications are especially useful.