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VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses
journal contribution
posted on 2023-02-10, 04:49 authored by S Tichkule, Y Myung, MT Naung, BRE Ansell, AJ Guy, N Srivastava, S Mehra, SM Cacciò, I Mueller, Alyssa BarryAlyssa Barry, C van Oosterhout, B Pope, DB Ascher, AR JexAbstract
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.
History
Journal
Molecular biology and evolutionVolume
39Article number
ARTN msac196Location
United StatesPublisher DOI
ISSN
0737-4038eISSN
1537-1719Language
EnglishPublication classification
C1 Refereed article in a scholarly journalEditor/Contributor(s)
Teeling EIssue
9Publisher
OXFORD UNIV PRESSUsage metrics
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Keywords
Science & TechnologyLife Sciences & BiomedicineBiochemistry & Molecular BiologyEvolutionary BiologyGenetics & Heredityprotein structurevariant interpretationmulti-dimensional analysisdata visualizationpopulation geneticsevolutionPROTEIN-STRUCTUREGENERATIONDATABASEERYTHROCYTEMUTATIONSINVASIONPLATFORMSNPSGenomicsGenotypePhenotypePolymorphism, GeneticSoftwareHuman GenomeBiotechnologyGenetics2 Aetiology2.1 Biological and endogenous factorsGeneric health relevanceEvolutionary BiologyGeneticsBiochemistry and Cell Biology not elsewhere classified
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