ArticleBMC bioinformatics2019
Alignment-free genomic sequence comparison using FCGR and signal processing.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Genome-wide pervasiveness and localized variation of [Formula: see text]-mer-based genomic signatures in eukaryotes.Scientific reports · 2026Article
- Predicting VNN resistance in European sea bass using machine learning on high dimensional low sample size data.Frontiers in bioinformatics · 2026Article
- Overview and Prospects of DNA Sequence Visualization.International journal of molecular sciences · 2025Review
- CGRclust: Chaos Game Representation for twin contrastive clustering of unlabelled DNA sequences.BMC genomics · 2024Article
- Genome analysis through image processing with deep learning models.Journal of human genetics · 2024Review
- Exploring geometry of genome space via Grassmann manifolds.Innovation (Cambridge (Mass.)) · 2024Article
- PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification.PloS one · 2024Article
- Polarization- and Chaos-Game-Based Fingerprinting of Molecular Targets of Listeria Monocytogenes Vaccine and Fully Virulent Strains.Current issues in molecular biology · 2023Article
- A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-CoV-2 genomes.BMC genomics · 2023Article
- In silico identification of multiple conserved motifs within the control region of Culicidae mitogenomes.Scientific reports · 2022Article
- Interpreting alignment-free sequence comparison: what makes a score a good score?NAR genomics and bioinformatics · 2022Article
- FFP: joint Fast Fourier transform and fractal dimension in amino acid property-aware phylogenetic analysis.BMC bioinformatics · 2022Article
- 4D-Dynamic Representation of DNA/RNA Sequences: Studies on Genetic Diversity ofLife (Basel, Switzerland) · 2022Article
- Detection of intra-family coronavirus genome sequences through graphical representation and artificial neural network.Expert systems with applications · 2022Article
- WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs.PloS one · 2022Article
- Non-standard bioinformatics characterization of SARS-CoV-2.Computers in biology and medicine · 2021Article
- Chaos game representation and its applications in bioinformatics.Computational and structural biotechnology journal · 2021Review
- A deep learning model for plant lncRNA-protein interaction prediction with graph attention.Molecular genetics and genomics : MGG · 2020Article
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1 author.
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Abstract
backgroundAlignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes of deducing "nearby" species in a reference data set, or for constructing phylogenetic trees.
resultsWe describe one such method that gives quite strong results. We use the Frequency Chaos Game Representation (FCGR) to create images from such sequences, We then reduce dimension, first using a Fourier trig transform, followed by a Singular Values Decomposition (SVD). This gives vectors of modest length. These in turn are used for fast sequence lookup, construction of phylogenetic trees, and classification of virus genomic data. We illustrate the accuracy and scalability of this approach on several benchmark test sets.
conclusionsThe tandem of FCGR and dimension reductions using Fourier-type transforms and SVD provides a powerful approach for alignment-free genomic comparison. Results compare favorably and often surpass best results reported in prior literature. Good scalability is also observed.
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