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Title:
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Choi-Williams distribution to describe coding and non-coding regions in primary transcript pre-mRNA
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Author:
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Melia, Umberto; Vallverdú, Montserrat; Clarià Sancho, Francisco; Gallardo, Juan J.; Perera, Alexandre; Caminal Magrans, Pere
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Notes:
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En este trabajo se ha elegido un método numérico de conversión de la secuencia de nucleótidos pre-mRNA basado en la información termodinámica, asociada a los cambios de energía libre de esta secuencia, durante la formación de una estructura dúplex de ADN o ARN. Con esta secuencia numérica se han caracterizado las regiones codificantes (exones) y las regiones no codificantes (intrones) utilizando una metodología basada en la representación tiempo-frecuencia (RTF). Esto ha permitido observar la evolución de la periodicidad y las componentes de frecuencia a lo largo del tiempo, introduciendo más variables relacionadas con las secuencias de genes en comparación con un análisis de Fourier. Se ha encontrado que variables específicas de frecuencia y de potencia calculadas en las distintas bandas de frecuencia estudiadas ha hecho posible la correcta clasificación entre los exones y los intrones con una precisión de más de 85%.
Deoxyribonucleic acid (DNA) information is discrete in both “time” (sequence positions) and “amplitude” (nucleotide values). This permits the use of signal processing techniques for its characterization. The conversion of DNA nucleotide symbols into discrete numerical values enables signal processing to be employed to solve problems related to sequence analysis, such as finding coding sequences. In this work, a numerical conversion method was
chosen based on the thermodynamic data of free energy changes (ΔG°) of the formation of a duplex structure of DNA or ribonucleic acid (RNA), associated with the nucleotide sequence pre-mRNA (messenger RNA). The aim of this
work was to characterize coding regions (exons) from non-coding regions (introns) using a methodology based on time-frequency representation (TFR). This permits the observation of the evolution of the periodicity and frequency components with time, introducing more variables related to the gene sequences compared to those used in traditional
fast Fourier transform analysis. The parameters calculated from TFR are instantaneous frequency and instantaneous power. It was found that instantaneous frequency and power variables in different frequency bands allowed the correct classification between exons and introns with a prediction accuracy of more than 85%. |
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Subject(s):
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-Procesado de señales biomédicas
-Ingeniería biomédica
-Bioinformatics (genome) databases,
-Classification and feature extraction
-Stochastic processes
-Time series analysis
-Enginyeria biomèdica
-Biomedical engineering |
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Rights:
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(c) Biomedical Engineering Society , 2013
info:eu-repo/semantics/restrictedAccess |
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Document type:
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Article
publishedVersion |
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Published by:
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Biomedical Engineering Society (Taiwan)
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