ArticleBMC bioinformatics2006
Genome-wide DNA polymorphism analyses using VariScan.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed.
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- Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes.Molecular biology and evolution · 2021Article
- Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans.Genome biology and evolution · 2021Article
- Episodes of gene flow and selection during the evolutionary history of domesticated barley.BMC genomics · 2021Article
- Rapid Spread of Mutant Alleles in Worldwide SARS-CoV-2 Strains Revealed by Genome-Wide Single Nucleotide Polymorphism and Variation Analysis.Genome biology and evolution · 2021Article
- Genome-Wide Association Study Reveals Complex Genetic Architecture of Cadmium and Mercury Accumulation and Tolerance Traits inFrontiers in plant science · 2021Article
- Genetic Differentiation of Reintroduced Père David's Deer (Frontiers in genetics · 2021Article
- Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations ofFrontiers in microbiology · 2021Article
- Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2.Scientific reports · 2020Article
- Narrow genetic base shapes population structure and linkage disequilibrium in an industrial oilseed crop, Brassica carinata A. Braun.Scientific reports · 2020Article
- Discordant evolution of mitochondrial and nuclear yeast genomes at population level.BMC biology · 2020Article
19 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
backgroundDNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis.
resultsWe have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers.
conclusionVariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.
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