ArticleMolecular biology and evolution2022
VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Host genotype and sex shape influenza evolution and defective viral genomes.Nature communications · 2026Article
- Host range expansion of asexual parasite can be explained by loss of adaptions in Muller's Ratchet.Nature communications · 2025Article
- Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease.Human molecular genetics · 2024Article
- 3DVizSNP: a tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D.BMC bioinformatics · 2023Article
- AlphaFold, allosteric, and orthosteric drug discovery: Ways forward.Drug discovery today · 2023Review
- Novel biological insights revealed from the investigation of multiscale genome architecture.Computational and structural biotechnology journal · 2023Review
- Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens.PLoS computational biology · 2022Article
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14 authors.
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Abstract
Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fitness. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an individual or population, in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, analysis of diversity and selection, and 3D visualization of genotypic information encoded in Variant Call Format on AlphaFold2 protein models. VIVID enables the rapid assessment of genes of interest in the study of adaptive evolution and the genetic load, and it helps prioritizing targets for experimental validation. We demonstrate the utility of VIVID by exploring the evolutionary genetics of the parasitic protist Plasmodium falciparum, revealing geographic variation in the signature of balancing selection in potential targets of functional antibodies.
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