PUMA
Istituto di Scienza e Tecnologie dell'Informazione     
Vitale D., Kuruoglu E. E., Abul O. Long range correlations between nucleotide triplets in human chromosomes. This report is created from the Tirocinio work and thesis of Daniele Vitale. The work was started and carried out when all authors were with ISTI-CNR in 2008. Technical report, 2010.
 
 
Abstract
(English)
The study of statistical fluctuations in DNA sequences can reveal important characteristics of their organization. Particularly, in the last two decades, several studies have focused on the detection of Long Range Correlations (LRC) in DNA sequences, and on the study of particular long range dependence properties of nucleotides. Since protein coding is carried out by codons (nucleotide triplets), we conduct LRC analysis to see whether there is a long range correlation among nucleotide triplets. Our interest is not limited to auto correlations of single codons, but also extends to cross correlations over all possible pairs of nucleotide triplets. LRCs in DNA sequences are studied and quantified using two measures: the mutual information function and the correlation function. The analysis on nucleotide triplets reveal LRCs for the human Chromosomes 20 and 21. Moreover, some triplets that contain only nucleotides Adenine and Thymine are seen to exhibit correlation significantly higher than others.
Subject Bioinformatics
Genomics
DNA sequence analysis
Long range dependence
J.3 Life and Medical Sciences. Biology and genetics
G.3 Probability and Statistics. Correlation and regression analysis
E.4 Coding and Information Theory
92D10 Genetics
62M10 Time series, auto-correlation, regression, etc


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