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
| Autor: | Patrizia Bogani, Giuseppe Mersi, Paolo Grigolini, Leone Fronzoni, Elena Catanese, Luigi Palatella, Paolo Allegrini, Marcello Buiatti, Claudia Acquisti |
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| Rok vydání: | 2003 |
| Předmět: |
Genomics (q-bio.GN)
Training set integumentary system Statistical Mechanics (cond-mat.stat-mech) Computer science General Mathematics Applied Mathematics Existential quantification General Physics and Astronomy FOS: Physical sciences Statistical and Nonlinear Physics Condensed Matter - Soft Condensed Matter Genome Low complexity Correlation FOS: Biological sciences Entropy (information theory) Soft Condensed Matter (cond-mat.soft) Quantitative Biology - Genomics Algorithm Condensed Matter - Statistical Mechanics |
| DOI: | 10.48550/arxiv.cond-mat/0310649 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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