VIVID: a web application for variant interpretation and visualisation in multidimensional analyses
- Author(s)
- Tichkule, S; Myung, Y; Naung, MT; Ansell, BRE; Guy, AJ; Srivastava, N; Mehra, S; Cacciò, SM; Mueller, I; Barry, AE; van Oosterhout, C; Pope, B; Ascher, DB; Jex, AR;
- Journal Title
- Molecular Biology and Evolution
- Publication Type
- epub ahead of print
- 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 3-dimensional (3D) visualisation of genotypic information encoded in Variant Call Format (VCF) 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 prioritising 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.
- Publisher
- Oxford Academic
- Research Division(s)
- Population Health And Immunity
- PubMed ID
- 36103257
- Publisher's Version
- https://doi.org/10.1093/molbev/msac196
- Open Access at Publisher's Site
https://doi.org/10.1093/molbev/msac196- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2022-09-19 02:39:17
Last Modified: 2022-09-23 10:00:04