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 NonStationarity 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.

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 / C.ACQUISTI; P.ALLEGRINI;P.BOGANI; M.BUIATTI; E.CATANESE; L.FRONZONI; P.GRIGOLINI; G.MERSI;L.PALATELLA. - In: CHAOS, SOLITONS AND FRACTALS. - ISSN 0960-0779. - STAMPA. - 20:(2004), pp. 127-137.

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

BOGANI, PATRIZIA;BUIATTI, MARCELLO;
2004

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 NonStationarity 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.
2004
20
127
137
C.ACQUISTI; P.ALLEGRINI;P.BOGANI; M.BUIATTI; E.CATANESE; L.FRONZONI; P.GRIGOLINI; G.MERSI;L.PALATELLA
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Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/307761
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