ArticleProceedings of the National Academy of Sciences of the United States of America2009
Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 72 citations in OpenAlex.
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- Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants.Current genomics · 2023Article
- Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method.Virus research · 2023Article
- Developments in the classification and nomenclature of arthropod-infecting large DNA viruses that contain pif genes.Archives of virology · 2023Article
- Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.Cell systems · 2022Article
- Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model.Bioinformatics advances · 2022Article
- Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin.Frontiers in microbiology · 2022Article
- Alignment-free sequence comparison for virus genomes based on location correlation coefficient.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Article
- Viruses Infecting the European Catfish (Viruses · 2021Review
- A network-based integrated framework for predicting virus-prokaryote interactions.NAR genomics and bioinformatics · 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
- KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis.Frontiers in bioengineering and biotechnology · 2020Article
- DisCVR: Rapid viral diagnosis from high-throughput sequencing data.Virus evolution · 2019Article
- Alignment-Free Sequence Analysis and Applications.Annual review of biomedical data science · 2018Article
- An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes.PloS one · 2018Article
- A novel fast vector method for genetic sequence comparison.Scientific reports · 2017Article
- Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer.Scientific reports · 2017Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The vast sequence divergence among different virus groups has presented a great challenge to alignment-based sequence comparison among different virus families. Using an alignment-free comparison method, we construct the whole-proteome phylogeny for a population of viruses from 11 viral families comprising 142 large dsDNA eukaryote viruses. The method is based on the feature frequency profiles (FFP), where the length of the feature (l-mer) is selected to be optimal for phylogenomic inference. We observe that (i) the FFP phylogeny segregates the population into clades, the membership of each has remarkable agreement with current classification by the International Committee on the Taxonomy of Viruses, with one exception that the mimivirus joins the phycodnavirus family; (ii) the FFP tree detects potential evolutionary relationships among some viral families; (iii) the relative position of the 3 herpesvirus subfamilies in the FFP tree differs from gene alignment-based analysis; (iv) the FFP tree suggests the taxonomic positions of certain "unclassified" viruses; and (v) the FFP method identifies candidates for horizontal gene transfer between virus families.
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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.