ArticleScientific reports2017
Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer.
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 34 papers.
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Who cites it
34 citing papers in PubMed.
- Alignment-Free Genome Geometry and Mosaic Barcodes Characterize Modular Diversity in the Cacao Swollen Shoot Virus Complex.Viruses · 2026Article
- Alignment-freeJournal of clinical microbiology · 2026Article
- Deciphering 6-mer Spectra Distribution Rules in Coronavirus Genomes: Application to Comparative Genomic Analysis.International journal of molecular sciences · 2026Article
- Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay.bioRxiv : the preprint server for biology · 2026Article
- Isolation and characterization of goose astrovirus genotype 1 causing enteritis in goslings from Sichuan Province, China.BMC veterinary research · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing.BMC bioinformatics · 2024Article
- DiMA: sequence diversity dynamics analyser for viruses.Briefings in bioinformatics · 2024Article
- Article
- Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures.PloS one · 2024Article
- VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets.RNA (New York, N.Y.) · 2023Article
- Synonymous nucleotide changes drive papillomavirus evolution.Tumour virus research · 2022Review
- The complexity landscape of viral genomes.GigaScience · 2022Article
- CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices.Bioinformatics (Oxford, England) · 2022Article
- K-mer based prediction ofMicrobial genomics · 2022Article
- Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin.Frontiers in microbiology · 2022Article
- An Alignment-Independent Approach for the Study of Viral Sequence Diversity at Any Given Rank of Taxonomy Lineage.Biology · 2021Article
- Variable number tandem repeats mediate the expression of proximal genes.Nature communications · 2021Article
- PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses.Scientific reports · 2021Article
- Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes.BMC evolutionary biology · 2020Article
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5 authors.
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Abstract
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins. In this study, we used an alignment-free method that uses k-mers as genomic features for a large-scale comparison of complete viral genomes available in RefSeq. To determine the optimal feature length, k (an essential step in constructing a meaningful dendrogram), we designed a comprehensive strategy that combines three approaches: (1) cumulative relative entropy, (2) average number of common features among genomes, and (3) the Shannon diversity index. This strategy was used to determine k for all 3,905 complete viral genomes in RefSeq. The resulting dendrogram shows consistency with the viral taxonomy of the ICTV and the Baltimore classification of viruses.
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