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VIVID: a web application for variant interpretation and visualisation in multidimensional analyses [article]

Swapnil Tichkule, Yoochan Myung, Myo T Naung, Brendan RE Ansell, Andrew Guy, Namrata Srivastava, Somya Mehra, Simone M Caccio, Ivo Mueller, Alyssa E Barry, Cock van Oosterhout, Bernard Pope (+2 others)
2021 bioRxiv   pre-print
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  ...  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  ...  The complete nucleotide coding sequence of a gene in FASTA format. 2. A general feature format (GFF) file to extract genomic coordinates of the queried coding sequence and to map SNPs from 3.  ... 
doi:10.1101/2021.11.16.468904 fatcat:hvao7oyf6bcx7ku6uebao2734i

Computational Analysis of Rice Transcriptomic and Genomic Datasets in Search for SNPs Involved in Flavonoid Biosynthesis [chapter]

Rabiatul-Adawiah Zainal-Abidin, Zeti-Azura Mohamed-Hussein
2020 Recent Advances in Rice Research [Working Title]  
Different tools, algorithms and databases are available to analyze the ontology, metabolic and pathway at the molecular level in order to observe the effects of gene and protein expression.  ...  This chapter describes the computational approach used in analyzing rice transcriptomics and genomics data to identify and annotate potential single nucleotide polymorphism (SNPs) as potential biomarker  ...  This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in  ... 
doi:10.5772/intechopen.94876 fatcat:5tk2qhybgbc6pfyb66uenmofdm

VIVID: a web application for variant interpretation and visualisation in multidimensional analyses

Swapnil Tichkule, Yoochan Myung, Myo T Naung, Brendan R E Ansell, Andrew J Guy, Namrata Srivastava, Somya Mehra, Simone M Cacciò, Ivo Mueller, Alyssa E Barry, Cock van Oosterhout, Bernard Pope (+2 others)
2022
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  ...  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  ...  The complete nucleotide coding sequence of a gene in FASTA format. 2. A general feature format (GFF) file to extract genomic coordinates of the queried coding sequence and to map SNPs from 3.  ... 
doi:10.1093/molbev/msac196 pmid:36103257 pmcid:PMC9514033 fatcat:lgqomqu7tfgfbibyxx4zrvifkm