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- Ivo Grosse, Pedro Bernaola-Galván, Pedro Carpena, Ramón Román-Roldán, Jose Oliver, H Eugene Stanley
- Physical review. E, Statistical, nonlinear, and…
- 2002

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)

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)

A segmentation algorithm based on the Jensen-Shannon entropic divergence is used to decompose long-range 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)

Alu retrotransposons do not show a homogeneous distribution over the human genome but have a higher density in GC-rich (H) than in AT-rich (L) isochores. However, since they preferentially insert into the L isochores, the question arises: What is the evolutionary mechanism that shifts the Alu density maximum from L to H isochores? To disclose the role… (More)

MOTIVATION
DNA sequences are formed by patches or domains of different nucleotide composition. In a few simple sequences, domains can simply be identified by eye; however, most DNA sequences show a complex compositional heterogeneity (fractal structure), which cannot be properly detected by current methods. Recently, a computationally efficient segmentation… (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)

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)

- José L Oliver, Pedro Carpena, Ramón Román-Roldán, Trinidad Mata-Balaguer, Andrés Mejías-Romero, Michael Hackenberg +1 other
- Gene
- 2002

The human genome is a mosaic of isochores, which are long DNA segments (z.Gt;300 kbp) relatively homogeneous in G+C. Human isochores were first identified by density-gradient ultracentrifugation of bulk DNA, and differ in important features, e.g. genes are found predominantly in the GC-richest isochores. Here, we use a reliable segmentation method to… (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.

- Qianli D Y Ma, Ronny P Bartsch, Pedro Bernaola-Galván, Mitsuru Yoneyama, Plamen Ch Ivanov
- Physical review. E, Statistical, nonlinear, and…
- 2010

Detrended fluctuation analysis (DFA) is an improved method of classical fluctuation analysis for nonstationary signals where embedded polynomial trends mask the intrinsic correlation properties of the fluctuations. To better identify the intrinsic correlation properties of real-world signals where a large amount of data is missing or removed due to… (More)