Pedro Bernaola-Galván

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A segmentation algorithm based on the Jensen-Shannon entropic divergence is used to decompose longrange correlated DNA sequences into statistically significant, compositionally homogeneous patches. By adequately setting the significance level for segmenting the sequence, the underlying power-law distribution of patch lengths can be revealed. Some of the(More)
We study statistical properties of the Jensen-Shannon divergence D, which quantifies the difference between probability distributions, and which has been widely applied to analyses of symbolic sequences. We present three interpretations of D in the framework of statistical physics, information theory, and mathematical statistics, and obtain approximations(More)
We present a new computational approach to finding borders between coding and noncoding DNA. This approach has two features: (i) DNA sequences are described by a 12-letter alphabet that captures the differential base composition at each codon position, and (ii) the search for the borders is carried out by means of an entropic segmentation method which uses(More)
Recursive segmentation is a procedure that partitions a DNA sequence into domains with a homogeneous composition of the four nucleotides A, C, G and T. This procedure can also be applied to any sequence converted from a DNA sequence, such as to a binary strong(G + C)/weak(A + T) sequence, to a binary sequence indicating the presence or absence of the(More)
-The analysis of DNA sequences through information theory methods is reviewed from the beginning in the 70s. The subject is addressed within a broad context, describing in some detail the cornerstone contributions in the field. The emerging interest concerning long-range correlations and the mosaic structure of DNA sequences is considered from our own point(More)
Isochores are long genome segments homogeneous in G+C. Here, we describe an algorithm (IsoFinder) running on the web (http://bioinfo2.ugr.es/IsoF/isofinder.html) able to predict isochores at the sequence level. We move a sliding pointer from left to right along the DNA sequence. At each position of the pointer, we compute the mean G+C values to the left and(More)
Analytical DNA ultracentrifugation revealed that eukaryotic genomes are mosaics of isochores: long DNA segments (>>300 kb on average) relatively homogeneous in G+C. Important genome features are dependent on this isochore structure, e.g. genes are found predominantly in the GC-richest isochore classes. However, no reliable method is available to rigorously(More)
Entropy and relative entropy are proposed as features extracted from symbol sequences. Firstly, a proper Iterated Function System is driven by the sequence, producing a fractal-like representation (CSR) with a low computational cost. Then, two entropic measures are applied to the CSR histogram of the CSR and theoretically justified. Examples are included.
When investigating the dynamical properties of complex multiple-component physical and physiological systems, it is often the case that the measurable system's output does not directly represent the quantity we want to probe in order to understand the underlying mechanisms. Instead, the output signal is often a linear or nonlinear function of the quantity(More)
Using a generalization of the level statistics analysis of quantum disordered systems, we present an approach able to extract automatically keywords in literary texts. Our approach takes into account not only the frequencies of the words present in the text but also their spatial distribution along the text, and is based on the fact that relevant words are(More)