ArticleViruses2020
Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses.
Article in Viruses, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
- Complete sequence, analysis and organization of the Graphiphora augur granulovirus genome.BMC genomics · 2026Article
- Amplicon-based analyses of single-nucleotide polymorphisms reveal the genetic structure of a forest insect baculovirus.Virus evolution · 2025Article
- Transcriptome analysis of CpGV in midguts of type II resistant codling moth larvae and identification of contaminant infections by SNP mapping of RNA-Seq data.Journal of virology · 2024Article
- Genome Sequence of a Spodoptera frugiperda Multiple Nucleopolyhedrovirus Isolated from Fall Armyworm (Spodoptera frugiperda) in Nigeria, West Africa.Microbiology resource announcements · 2021Article
- Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition.Molecular biology and evolution · 2021Article
- Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus.Viruses · 2021Article
- Transcriptome of Cydia pomonella granulovirus in susceptible and type I resistant codling moth larvae.The Journal of general virology · 2021Article
- Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation.Virus evolution · 2021Article
- Genome Analysis of a Novel Clade bViruses · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Natural isolates of baculoviruses (as well as other dsDNA viruses) generally consist of homogenous or heterogenous populations of genotypes. The number and positions of single nucleotide polymorphisms (SNPs) from sequencing data are often used as suitable markers to study their genotypic composition. Identifying and assigning the specificities and frequencies of SNPs from high-throughput genome sequencing data can be very challenging, especially when comparing between several sequenced isolates or samples. In this study, the new tool "bacsnp", written in R programming langue, was developed as a downstream process, enabling the detection of SNP specificities across several virus isolates. The basis of this analysis is the use of a common, closely related reference to which the sequencing reads of an isolate are mapped. Thereby, the specificities of SNPs are linked and their frequencies can be used to analyze the genetic composition across the sequenced isolate. Here, the downstream process and analysis of detected SNP positions is demonstrated on the example of three baculovirus isolates showing the fast and reliable detection of a mixed sequenced sample.
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