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
✍ Scribed by Claudia Acquisti; Paolo Allegrini; Patrizia Bogani; Marcello Buiatti; Elena Catanese; Leone Fronzoni; Paolo Grigolini; Giuseppe Mersi; Luigi Palatella
- Publisher
- Elsevier Science
- Year
- 2004
- Tongue
- English
- Weight
- 220 KB
- Volume
- 20
- Category
- Article
- ISSN
- 0960-0779
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✦ Synopsis
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.