ArticleGene2014
K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.
Article in Gene, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Tracking Down the Evolution of Microorganisms by Exhaustive Bottom-Up Analysis of Proteomes.International journal of molecular sciences · 2025Article
- Energy entropy vector: a novel approach for efficient microbial genomic sequence analysis and classification.Briefings in bioinformatics · 2025Article
- Taxonomic quasi-primes: peptides charting lineage-specific adaptations and disease-relevant loci.Protein science : a publication of the Protein Society · 2025Article
- The grand biological universe: A comprehensive geometric construction of genome space.Innovation (Cambridge (Mass.)) · 2025Article
- Unraveling diversity by isolating peptide sequences specific to distinct taxonomic groups.bioRxiv : the preprint server for biology · 2025Article
- DeepRice6mA: A convolutional neural network approach for 6mA site prediction in the rice Genome.PloS one · 2025Article
- Reconstruction of masked sequencesPeerJ · 2025Article
- The optimal metric for viral genome space.Computational and structural biotechnology journal · 2024Article
- AntiBinder: utilizing bidirectional attention and hybrid encoding for precise antibody-antigen interaction prediction.Briefings in bioinformatics · 2024Article
- Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection.Briefings in bioinformatics · 2024Article
- Article
- 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
- Classification ofiScience · 2024Article
- Automated recognition of chromosome fusion using an alignment-free natural vector method.Frontiers in genetics · 2024Article
- A novel method for identifying key genes in macroevolution based on deep learning with attention mechanism.Scientific reports · 2023Article
- Comparative study of encoded and alignment-based methods for virus taxonomy classification.Scientific reports · 2023Article
- Generating Minimal Models of H1N1 NS1 Gene Sequences Using Alignment-Based and Alignment-Free Algorithms.Genes · 2023Article
- Exploring the dynamic variations of viral genomes via a novel genetic network.Molecular phylogenetics and evolution · 2022Article
- Identification of HIV Rapid Mutations Using Differences in Nucleotide Distribution over Time.Genes · 2022Article
- Feature extraction based on microstate sequences for EEG-based emotion recognition.Frontiers in psychology · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.