Genomic signal processing

Anastassiou, Dimitris

doi:10.1109/79.939833

Cited by 392 publications

(316 citation statements)

References 24 publications

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“…However, that this is possible mainly in cases where the segments of sequences under investigation incorporate coding regions. It has been observed that such segments exhibit many local periodicities [2,23]. Further, according to the uncertainty principle, and to Gabor's theory of signal representation in combined spaces, the wider the window the better is the frequency resolution (i.e., the definition of the index) and vice versa [14].…”

Section: Storage and Indexing Of Dna Sequencesmentioning

confidence: 99%

“…We have compared our method with the methods of [32,2] for DNA sequences, and with those presented in [6] for protein sequences. We show the advantages of using multiwindow Gabor representations for detecting local periodicities, storing and searching for sequences.…”

Section: Comparison With Wavelet-based Techniquesmentioning

confidence: 99%

“…Of these, we will utilize and compare two techniques employed most commonly. In [2], the author introduced a technique that explicitly preserves the complementary properties of the bases, and also maps the character string into a numerical sequence. We adopt this technique of mapping A; G; T; and C into 1 þ j; À1 þ j; 1 À j; and À1 À j, respectively.…”

Section: Introductionmentioning

confidence: 99%

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Macromolecular sequence analysis using multiwindow Gabor representations

Subbanna¹,

Zeevi²

2008

Signal Processing

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Multiwindow Gabor representations highlight fingerprints suitable for indexing of macromolecules, based on their local periodic structures. This paper presents a technique for analysis, and comparison of DNA and protein sequences. We use local periodicities to compare sequences and develop techniques that can compare the similarity between sequences in the combined space. We further show that using correlation, and absolute error minimization between the query sequence and sequences in the database, one can search for sequences very efficiently. Thus, from the viewpoint of indexing (and otherwise), macromolecules are much simpler to deal with than images, in that a much more limited, and well-defined dictionary is sufficient for labeling the molecules. r

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Section: Storage and Indexing Of Dna Sequencesmentioning

confidence: 99%

Section: Comparison With Wavelet-based Techniquesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Macromolecular sequence analysis using multiwindow Gabor representations

Subbanna¹,

Zeevi²

2008

Signal Processing

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“…However, several other different mappings have been proposed (see for example, Silverman and Linsker (1986); Jeffrey (1990); Zhang and Zhang (1994); Buldyrev et al (1995); Anastassiou (2001) In a previous work, we explored the inter-nucleotide (IN) distance, the distance to the first occurrence of the same symbol, to perform a comparative analysis between species (Afreixo et al, 2009). In this work, we present a new DNA numerical profile and a new mapping to explore the correlation structure of DNA: the distance to the nearest dissimilar (ND) nucleotide.…”

Section: Introductionmentioning

confidence: 99%

Genome analysis with distance to the nearest dissimilar nucleotide

Afreixo

Bastos

Pinho

et al. 2011

Journal of Theoretical Biology

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DNA may be represented by sequences of four symbols, but it is often useful to convert those symbols into real or complex numbers for further analysis.Several mapping schemes have been used in the past, but most of them seem to be unrelated to any intrinsic characteristic of DNA. The objective of this work was to study a mapping scheme that is directly related to DNA characteristics, and that could be useful in discriminating between different species.Recently, we have proposed a methodology based on the inter-nucleotide distance, which proved to contribute to the discrimination among species. In this paper, we introduce a new distance, the distance to the nearest dissimilar nucleotide, which is the distance of a nucleotide to first occurrence of a different nucleotide. This distance is related to the repetition structure of single nucleotides. Using the information resulting from the concatenation of the distance to the nearest dissimilar and the inter-nucleotide distance, we found that this new distance brings additional discriminative capabilities. Preprint submitted to Journal of Theoretical BiologyJanuary 31, 2011 This suggests that the distance to the nearest dissimilar nucleotide might contribute with useful information about the evolution of the species.

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“…En este contexto una solución viable es la implementación de herramientas matemáticas propias del procesamiento de señales genómicas [9] . El procesamiento de señales genómicas es un área multidisciplinaria que utiliza herramientas propias del procesamiento digital de señales para extraer información con un significado biológico específico [10,11] Dentro de este campo, uno de los hallazgos más estudiados e importantes en las regiones codificantes de proteínas es la existencia de un pico en la frecuencia f/3 y la ausencia de este pico en las no codificantes [12,18] . Sin embargo, las regiones codificantes solo representan el 1% del genoma humano y por varios años el resto del genoma fue considerado ADN "basura" [19,20] .…”

Section: Introductionunclassified

Statistical analysis of the Fourier Spectra of the ENCODE regulatory regions

Paredes

Romo-Vázquez

Vélez-Pérez

et al.

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RESUMENEn la actualidad, nuevas bases de datos genómicos (secuencias de ADN) son puestas al alcance del dominio público para su análisis. La bioinformática ha desarrollado algoritmos para extraer información y características de dichas secuencias. Sin embargo, estos algoritmos bioinformáticos tienen limitaciones. Una alternativa es utilizar herramientas propias del procesamiento digital de señales (DSP) adaptadas a secuencias genómicas (procesamiento de señales genómicas -GSP). El presente trabajo versa sobre el análisis de los cuatro primeros momentos centrales (media, desviación estándar, asimetría y curtosis) y dos momentos estadísticos (mediana y varianza) de los espectros frecuenciales de las 15 Regiones Reguladoras (RRs) de la base de datos ENCODE con el objetivo de estudiar diferencias estadísticas y frecuencias características. La base de datos seleccionada es "mapeada". Luego, la FFT es calculada a estas señales genómicas y finalmente los momentos estadísticos son implementados. Los resultados muestran la existencia de 3 grupos de RRs utilizando la media, mediana y curtosis. La desviación estándar y la varianza, parecen no resaltar información importante. Finalmente, la asimetría revela un comportamiento homogéneo ante la presencia de valores atípicos en algunas RRs. Estas observaciones permiten inferir que la periodicidad dentro de la secuencia está relacionada o podría determinar la función biológica que desempeña la misma secuencia.

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Genomic signal processing

Cited by 392 publications

References 24 publications

Macromolecular sequence analysis using multiwindow Gabor representations

Macromolecular sequence analysis using multiwindow Gabor representations

Genome analysis with distance to the nearest dissimilar nucleotide

Statistical analysis of the Fourier Spectra of the ENCODE regulatory regions

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