We investigate on a possible way to connect the presence of low-complexity sequences (LCS) in DNA genomes and the non-stationary 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. (C) 2003 Elsevier Ltd. All rights reserved.

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

FRONZONI, LEONE;
2004-01-01

Abstract

We investigate on a possible way to connect the presence of low-complexity sequences (LCS) in DNA genomes and the non-stationary 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. (C) 2003 Elsevier Ltd. All rights reserved.
2004
Acquisti, C; Allegrini, P; Bogani, P; Buiatti, M; Catanese, E; Fronzoni, Leone; Grigolini, P; Mersi, G; Palatella, L.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11568/90689
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