ArticlePloS one2017
On DNA numerical representations for genomic similarity computation.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing.BMC bioinformatics · 2024Article
- Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA.Briefings in bioinformatics · 2023Article
- New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning.BMC bioinformatics · 2023Article
- Temporal convolutional network for a Fast DNA mutation detection in breast cancer data.PloS one · 2023Article
- DeepTSS: multi-branch convolutional neural network for transcription start site identification from CAGE data.BMC bioinformatics · 2022Article
- BoT-Net: a lightweight bag of tricks-based neural network for efficient LncRNA-miRNA interaction prediction.Interdisciplinary sciences, computational life sciences · 2022Article
- Hidden Information Revealed Using the Orthogonal System of Nucleic Acids.International journal of molecular sciences · 2022Article
- MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors.Briefings in bioinformatics · 2022Article
- Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture.PloS one · 2021Article
- Frequency spectra characterization of noncoding human genomic sequences.Genes & genomics · 2020Article
- Article
- Alignment-free genomic sequence comparison using FCGR and signal processing.BMC bioinformatics · 2019Article
- Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage.BMC bioinformatics · 2019Article
- Genetic similarity of biological samples to counter bio-hacking of DNA-sequencing functionality.Scientific reports · 2019Article
- Integrated entropy-based approach for analyzing exons and introns in DNA sequences.BMC bioinformatics · 2019Article
- ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels.BMC genomics · 2019Article
- A degeneration-reducing criterion for optimal digital mapping of genetic codes.Computational and structural biotechnology journal · 2019Article
- Rapid Bacterial Species Delineation Based on Parameters Derived From Genome Numerical Representations.Computational and structural biotechnology journal · 2019Article
- Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Genomic signal processing (GSP) refers to the use of signal processing for the analysis of genomic data. GSP methods require the transformation or mapping of the genomic data to a numeric representation. To date, several DNA numeric representations (DNR) have been proposed; however, it is not clear what the properties of each DNR are and how the selection of one will affect the results when using a signal processing technique to analyze them. In this paper, we present an experimental study of the characteristics of nine of the most frequently-used DNR. The objective of this paper is to evaluate the behavior of each representation when used to measure the similarity of a given pair of DNA sequences.
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