Frequency spectra characterization of noncoding human genomic sequences

Background Noncoding sequences have been demonstrated to possess regulatory functions. Its classification is challenging because they do not show well-defined nucleotide patterns that can correlate with their biological functions. Genomic signal processing techniques like Fourier transform have been...

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Bibliographic Details
Published in:Genes & genomics 2020, 42(10), , pp.1215-1226
Main Authors: Paredes, O., Romo-Vázquez, Rebeca, Román-Godínez, Israel, Vélez-Pérez, Hugo, Salido-Ruiz, Ricardo A., Morales, J. Alejandro
Format: Article
Language:English
Subjects:
Animal Genetics and Genomics
Biomedical and Life Sciences
Cell lines
Chromosomes
Fourier transforms
Genomes
Human Genetics
Learning algorithms
Life Sciences
Machine learning
Microbial Genetics and Genomics
Plant Genetics and Genomics
Regulatory sequences
Research Article
Signal processing
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Summary:Background Noncoding sequences have been demonstrated to possess regulatory functions. Its classification is challenging because they do not show well-defined nucleotide patterns that can correlate with their biological functions. Genomic signal processing techniques like Fourier transform have been employed to characterize coding and noncoding sequences. This transformation in a systematic whole-genome noncoding library, such as the ENCODE database, can provide evidence of a periodic behaviour in the noncoding sequences that correlates with their regulatory functions. Objective The objective of this study was to classify different noncoding regulatory regions through their frequency spectra. Methods We computed machine learning algorithms to classify the noncoding regulatory sequences frequency spectra. Results The sequences from different regulatory regions, cell lines, and chromosomes possessed distinct frequency spectra, and that machine learning classifiers (such as those of the support vector machine type) could successfully discriminate among regulatory regions, thus correlating the frequency spectra with their biological functions Conclusion Our work supports the idea that there are patterns in the noncoding sequences of the genome.
ISSN:1976-9571
2092-9293
DOI:10.1007/s13258-020-00980-2