VIVID: a web application for variant interpretation and visualisation in multidimensional analyses
Open accessPreprint — published as 10.1093/molbev/msac196 · Paper page
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Flagged first, then by citations
- Authors
- Tichkule, S., Myung, Y., Naung, M. T., Ansell, B. R. E., Guy, A. J., Srivastava, N., Mehra, S., Caccio, S. M., Mueller, I., Barry, A. E., van Oosterhout, C., Pope, B., Ascher, D. B., & Jex, A. R.
- Affiliations
- The University of Melbourne (AU)
- Baker Heart and Diabetes Institute (AU)
- Walter and Eliza Hall Institute of Medical Research (AU)
- RMIT University (AU)
- Monash University (AU)
- Burnet Institute (AU)
- The Royal Melbourne Hospital (AU)
- Corresponding author
- Tichkule, Swapnil
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- openRxiv
- Published
- 2021-11-19
- Volume
- 39
- Issue
- 9
- ISSN
- 0737-4038 (ISSN-L)
- PMC
- PMC9514033
- OpenAlex
- W4295761272
- Cited by
- 11
- References
- 1
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 5 · 2022: 3
- FWCI
- 1.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Figshare (submittedVersion, cc-by-nc)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by-nc)
- Funders
- Australian Government
- Australian Society for Parasitology
- RMIT University
- Medical Research Council
- National Health and Medical Research Council (1174405, 1194330, 1126395, 1155075)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- variant interpretation, variant visualization, web application, DNA variants, mutation mapping, conservation scores, deleterious variant prediction, balancing selection, adaptive evolution, genetic load, Plasmodium falciparum, 3D protein model, AlphaFold2, variant call format, population genetics, comparative genomics
- MeSH terms
- Genotype, Phenotype, Polymorphism, Genetic, Software, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
