ArticleScientific reports2017
A novel fast vector method for genetic sequence comparison.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Energy entropy vector: a novel approach for efficient microbial genomic sequence analysis and classification.Briefings in bioinformatics · 2025Article
- Missing value replacement in strings and applications.Data mining and knowledge discovery · 2025Article
- Hyperdimensional computing: A fast, robust, and interpretable paradigm for biological data.PLoS computational biology · 2024Review
- Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification.PloS one · 2024Article
- CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model.Frontiers in microbiology · 2024Article
- A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-CoV-2 genomes.BMC genomics · 2023Article
- Generating Minimal Models of H1N1 NS1 Gene Sequences Using Alignment-Based and Alignment-Free Algorithms.Genes · 2023Article
- Compression-Complexity Measures for Analysis and Classification of Coronaviruses.Entropy (Basel, Switzerland) · 2022Article
- WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs.PloS one · 2022Article
- Deformity Index: A Semi-Reference Clade-Based Quality Metric of Phylogenetic Trees.Journal of molecular evolution · 2021Article
- High-Throughput Genotyping Technologies in Plant Taxonomy.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A new graph-theoretic approach to determine the similarity of genome sequences based on nucleotide triplets.Genomics · 2020Article
- Similarity Studies of Corona Viruses through Chaos Game Representation.Computational molecular bioscience · 2020Article
- Positional Correlation Natural Vector: A Novel Method for Genome Comparison.International journal of molecular sciences · 2020Article
- SWeeP: representing large biological sequences datasets in compact vectors.Scientific reports · 2020Article
- Alignment-free genomic sequence comparison using FCGR and signal processing.BMC bioinformatics · 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
- Alignment-free method for DNA sequence clustering using Fuzzy integral similarity.Scientific reports · 2019Article
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4 authors.
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Abstract
With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for sequence analysis. Among these methods, many sorts of feature vector methods are established and applied to reconstruction of species phylogeny. The vectors basically consist of some typical numerical features for certain biological problems. The features may come from the primary sequences, secondary or three dimensional structures of macromolecules. In this study, we propose a novel numerical vector based on only primary sequences of organism to build their phylogeny. Three chemical and physical properties of primary sequences: purine, pyrimidine and keto are also incorporated to the vector. Using each property, we convert the nucleotide sequence into a new sequence consisting of only two kinds of letters. Therefore, three sequences are constructed according to the three properties. For each letter of each sequence we calculate the number of the letter, the average position of the letter and the variation of the position of the letter appearing in the sequence. Tested on several datasets related to mammals, viruses and bacteria, this new tool is fast in speed and accurate for inferring the phylogeny of organisms.
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