VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses.

Autor:	Tichkule S; Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.; Department of Medical Biology, University of Melbourne, Melbourne, Australia., Myung Y; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Australia.; Computational Biology and Clinical Informatics, Baker Heart and Diabetes, Melbourne, Australia., Naung MT; Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.; Department of Medical Biology, University of Melbourne, Melbourne, Australia., Ansell BRE; Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia., Guy AJ; School of Science, RMIT University, Melbourne, Australia., Srivastava N; Department of Data Science and AI, Monash University, Melbourne, Australia., Mehra S; Life Sciences Discipline, Burnet Institute, Melbourne, Australia., Cacciò SM; Department of Infectious Disease, Istituto Superiore di Sanità, Rome, Italy., Mueller I; Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia., Barry AE; Life Sciences Discipline, Burnet Institute, Melbourne, Australia.; Institute of Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Australia., van Oosterhout C; School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK., Pope B; Melbourne Bioinformatics, University of Melbourne, Melbourne, Australia.; Australian BioCommons, Sydney, Australia.; Department of Clinical Pathology, University of Melbourne, Melbourne, Australia.; Department of Surgery (Royal Melbourne Hospital), University of Melbourne, Melbourne, Australia., Ascher DB; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Australia.; Computational Biology and Clinical Informatics, Baker Heart and Diabetes, Melbourne, Australia., Jex AR; Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.; Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Australia.
Jazyk:	angličtina
Zdroj:	Molecular biology and evolution [Mol Biol Evol] 2022 Sep 01; Vol. 39 (9).
DOI:	10.1093/molbev/msac196
Abstrakt:	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. (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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