In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

Claudia Acquisti; Paolo Allegrini; Patrizia Bogani; Marcello Buiatti; Elena Catanese; Leone Fronzoni; Paolo Grigolini; Giuseppe Mersi; Luigi Palatella

doi:10.1016/s0960-0779(03)00435-1

arXiv · cond-mat/0310649

In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures

Claudia Acquisti·Paolo Allegrini·Patrizia Bogani·Marcello Buiatti·Elena Catanese·Leone Fronzoni·Paolo Grigolini·Giuseppe Mersi·Luigi Palatella

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Abstract

We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function, we use a new technique, called Non-Stationarity Entropic Index (NSEI) method, and we prove that this technique is an efficient way to detect functional changes with respect to a random baseline. The remarkable aspect is that NSEI does not imply any training data or fitting parameter, the only arbitrarity being the choice of a marker in the sequence. We make this choice on the basis of biological information about LCS distributions in genomes. We show that there exists a correlation between changing the amount in LCS and the ratio of long- to short-range correlation.

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Claudia Acquisti, Paolo Allegrini, Patrizia Bogani, Marcello Buiatti, Elena Catanese, Leone Fronzoni, Paolo Grigolini, Giuseppe Mersi, Luigi Palatella. 2003-10-28. In the search for the low-complexity sequences in prokaryotic and eukaryotic genomes: how to derive a coherent picture from global and local entropy measures. https://doi.org/10.1016/s0960-0779(03)00435-1

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