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A complexity measure for symbolic sequences and applications to DNA [article]

Ana P. Majtey, Ramon Roman-Roldan, Pedro W. Lamberti
2006 arXiv   pre-print
We introduce a complexity measure for symbolic sequences. Starting from a segmentation procedure of the sequence, we define its complexity as the entropy of the distribution of lengths of the domains of relatively uniform composition in which the sequence is decomposed. We show that this quantity verifies the properties usually required for a "good" complexity measure. In particular it satisfies the one hump property, is super-additive and has the important property of being dependent of the
more » ... el of detail in which the sequence is analyzed. Finally we apply it to the evaluation of the complexity profile of some genetic sequences.
arXiv:physics/0606113v1 fatcat:mfszif4hf5h75pju4vtx6yxs7u

Decomposition of DNA Sequence Complexity

Pedro Bernaola-Galván, José L. Oliver, Ramón Román-Roldán
1999 Physical Review Letters  
Profiles of sequence compositional complexity provide a view of the spatial heterogeneity of symbolic sequences at different levels of detail. Sequence compositional complexity profiles are here decomposed into partial profiles using the branching property of the Shannon entropy. This decomposition shows the complexity contributed by each individual symbol or group of symbols. In particular, we apply this method to the mapping rules (symbol groupings) commonly used in DNA sequence analysis. We
more » ... ind that strong-weak bindings are remarkable homogeneously distributed as compared to purine pyrimidine, and that A and T are the most heterogeneous distributed bases.
doi:10.1103/physrevlett.83.3336 fatcat:nn2ikxnl3zbw5djvsrahgw3jbe


Abdessamad Ben Hamza, Pedro L. Luque-Escamilla, José Martínez-Aroza, Ramón Román-Roldán
2012 Journal of Mathematical Imaging and Vision  
Ramón Román Roldán is Professor of Applied Physics at the University of Granada, Spain.  ... 
doi:10.1023/a:1008395514426 fatcat:p4frqksmq5brfn5tyaghehdmse

Isochore chromosome maps of eukaryotic genomes

José L Oliver, Pedro Bernaola-Galván, Pedro Carpena, Ramón Román-Roldán
2001 Gene  
., 1998; Román-Roldán et al., 1998) .  ...  Binary (S/W, R/Y) as well as quaternary (A,T,C,G) alphabets can be used in segmenting DNA sequences (Bernaola-Galván et al., 1996; Román-Roldán et al., 1998; Oliver et al., 1999) .  ... 
doi:10.1016/s0378-1119(01)00641-2 pmid:11591471 fatcat:h5hgthldzrbidj5gxbqt2a76ki

Application of information theory to DNA sequence analysis: A review

Ramón Román-Roldán, Pedro Bernaola-Galván, JoséL Oliver
1996 Pattern Recognition  
ROMA, N-ROLDAN et al. rest in the subject, aided by the great increase in sequence data generated by genome projects.  ... 
doi:10.1016/0031-3203(95)00145-x fatcat:7b3vw2gvsrg63nsrmcxhawzyku

Sequence Compositional Complexity of DNA through an Entropic Segmentation Method

Ramón Román-Roldán, Pedro Bernaola-Galván, José L. Oliver
1998 Physical Review Letters  
A new complexity measure, based on the entropic segmentation of DNA sequences into compositionally homogeneous domains, is proposed. Sequence compositional complexity (SCC) deals directly with the complex heterogeneity in nonstationary DNA sequences. The plot of SCC as a function of significance level provides a profile of sequence structure at different length scales. SCC is found to be higher in sequences with long-range correlation than those without, and higher in noncoding sequences than
more » ... ding sequences. Furthermore, a general agreement is found between the SCC of the DNA sequence, on one hand, and the biological complexity of the organism, on the other, attributable to an increasingly complex organization of noncoding DNA over the course of evolution. [S0031-9007(97)05210-1]
doi:10.1103/physrevlett.80.1344 fatcat:shedicyx7zfpljvk6qhv6eespe

Isochore chromosome maps of the human genome

José L Oliver, Pedro Carpena, Ramón Román-Roldán, Trinidad Mata-Balaguer, Andrés Mejı́as-Romero, Michael Hackenberg, Pedro Bernaola-Galván
2002 Gene  
The human genome is a mosaic of isochores, which are long DNA segments (≫300 kbp) relatively homogeneous in G+C. Human isochores were first identified by densitygradient 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 partition the longest contigs in the human genome draft sequence into long homogeneous genome regions (LHGRs), thereby revealing the isochore structure
more » ... of the human genome. The advantages of the isochore maps presented here are: (1) sequence heterogeneities at different scales are shown in the same plot; (2) pair-wise compositional differences between adjacent regions are all statistically significant; (3) isochore boundaries are accurately defined to single base pair resolution; and (4) both gradual and abrupt isochore boundaries are simultaneously revealed. Taking advantage of the wide sample of genome sequence analyzed, we investigate the correspondence between LHGRs and true human isochores revealed through DNA centrifugation. LHGRs show many of the typical isochore features, mainly size distribution, G+C range, and proportions of the isochore classes. The relative density of genes, Alu and long interspersed nuclear element repeats and the different types of single nucleotide polymorphisms on LHGRs also coincide with expectations in true isochores. Potential applications of isochore maps range from the improvement of gene-finding algorithms to the prediction of linkage disequilibrium levels in association studies between marker genes and complex traits. The coordinates for the LHGRs identified in all the contigs
doi:10.1016/s0378-1119(02)01034-x pmid:12468093 fatcat:356nv4a6evd5tf755szt4ab72e

Median-type filters with model-based preselection masks

Lina García-Cabrera, M.José García-Salinas, Pedro L. Luque-Escamilla, José Martínez-Aroza, Juan F. Gómez Lopera, Ramón Román-Roldán
1996 Image and Vision Computing  
To remove impulsive noise, several variants of median-type filters are presented. They use some prior information provided by the probabilistic composition model of the class of the image being processed. This information is doubly applied; first, in elaborating a noise-estimation mask for the preselection of the pixels which must be filtered; and second, in the filtering process itself. The aim is to avoid the side-effect damage that median-type filters produce in processing the
more » ... d pixels. Experimental results are better than in the conventional median filter. * Corresponding author. 0262-8856/96/%15.00 0 1996 Elsevier Science B.V. All rights reserved PZZ SO262-8856(96)01084-O In this paper new median-type filters, called Mask-Model Filters, are introduced. The starting point is that a spatial filter damages some good pixels by itself, and this must be avoided. This problem is addressed by:
doi:10.1016/s0262-8856(96)01084-0 fatcat:5bc3ucr36jclbakk3uoxq6copi

A measure of quality for evaluating methods of segmentation and edge detection

Ramón Román-Roldán, Juan Francisco Gómez-Lopera, Chakir Atae-Allah, José Martı́nez-Aroza, Pedro Luis Luque-Escamilla
2001 Pattern Recognition  
A new measure of quality is proposed for evaluating the performance of available methods of image segmentation and edge detection. The technique is intended for the evaluation of low error results and features an objective assessment of discrepancy with respect to the theoretical edge, in tandem with subjective visual evaluation using both the neighbourhood and error-interaction criteria. The proposed mathematical model is extremely simple, even from the perspective of computational execution.
more » ... training of the measure has been put in practice, which uses visual evaluation of a set of error patterns by a team of observers. Encouraging results were obtained for a selection of test images, especially in relation to other recently proposed and/or currently employed quality measures.
doi:10.1016/s0031-3203(00)00052-2 fatcat:p3uleais7jdahdxgn2g55ryt4y

Finding Borders between Coding and Noncoding DNA Regions by an Entropic Segmentation Method

Pedro Bernaola-Galván, Ivo Grosse, Pedro Carpena, José L. Oliver, Ramón Román-Roldán, H. Eugene Stanley
2000 Physical Review Letters  
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 only the general statistical properties of coding DNA. We find that this method is highly accurate in finding borders between coding and
more » ... oding regions and requires no "prior training" on known data sets. Our results appear to be more accurate than those obtained with moving windows in the discrimination of coding from noncoding DNA.
doi:10.1103/physrevlett.85.1342 pmid:10991547 fatcat:svobdccc2zhlxlm2dp2qve4nne

Analysis of symbolic sequences using the Jensen-Shannon divergence

Ivo Grosse, Pedro Bernaola-Galván, Pedro Carpena, Ramón Román-Roldán, Jose Oliver, H. Eugene Stanley
2002 Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics  
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 of the mean, the variance, and the probability distribution of D in random, uncorrelated sequences. We present a segmentation method based on
more » ... D that is able to segment a nonstationary symbolic sequence into stationary subsequences, and apply this method to DNA sequences, which are known to be nonstationary on a wide range of different length scales.
doi:10.1103/physreve.65.041905 pmid:12005871 fatcat:6w327vbtorbzzbvvg4qh5qdqb4

Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria [article]

Andres Moya, Jose L. Oliver, Miguel Verdu, Luis Delaye, Vicente Arnau, Pedro Bernaola-Galvan, Rebeca de la Fuente, Wladimiro Diaz, Cristina Gomez-Martin, Francisco M. Gonzalez, Amparo Latorre, Ricardo Lebron (+1 others)
2020 bioRxiv   pre-print
. (•) = − ∑ 2 is the Shannon entropy of the distribution of relative frequencies of symbol occurrences {f} in the corresponding (sub)sequence (Román-Roldán et al., 1998) .  ... 
doi:10.1101/2020.01.29.924464 fatcat:pb55lttskvam7kkvgg2qqwgbgm

Compositional segmentation and long-range fractal correlations in DNA sequences

Pedro Bernaola-Galván, Ramón Román-Roldán, José L. Oliver
1996 Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics  
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 identified DNA domains were uncorrelated, but most of them continued to display long-range correlations even after several steps of recursive
more » ... gmentation, thus indicating a complex multi-length-scaled structure for the sequence. On the other hand, by separately shuffling each segment, or by randomly rearranging the order in which the different segments occur in the sequence, shuffled sequences preserving the original statistical distribution of patch lengths were generated. Both types of random sequences displayed the same correlation scaling exponents as the original DNA sequence, thus demonstrating that neither the internal structure of patches nor the order in which these are arranged in the sequence is critical; therefore, long-range correlations in nucleotide sequences seem to rely only on the power-law distribution of patch lengths.
doi:10.1103/physreve.53.5181 pmid:9964850 fatcat:adekqmbbpbheniuzk3hdltmao4

Driven progressive evolution of genome sequence complexity in Cyanobacteria

Andrés Moya, José L. Oliver, Miguel Verdú, Luis Delaye, Vicente Arnau, Pedro Bernaola-Galván, Rebeca de la Fuente, Wladimiro Díaz, Cristina Gómez-Martín, Francisco M. González, Amparo Latorre, Ricardo Lebrón (+1 others)
2020 Scientific Reports  
Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen
more » ... metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven—the minimum, ancestor–descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.
doi:10.1038/s41598-020-76014-4 pmid:33149190 fatcat:7xo5xpq6enfhvlh4bnhognhnqq

Page 405 of National Register of Prominent Americans and International Notables Vol. , Issue [page]

1972 National Register of Prominent Americans and International Notables  
., Roman Cath. Ch.; (c) Prominent Cit- izen Awd.-Lions C. 1968, Notable Wom. of Yr. 1970; (L) W.W. of Am.  ...  Wom.; [Mathematics-Lin- ear Algebra, Nonassociative Algebra]** +ROLDAN-BLAS, Israel; Professor of History, Social Sciences & Spanish, Inter Am.  ... 
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