Using the Integrated Genome Viewer to reveal amplicon‐derived polymorphism enriched at the phenylthiocarbamide locus in the teaching lab

2021 ◽  
Author(s):  
Eric D. Brenner ◽  
Paul E. Scheid ◽  
Justin DeGrazia ◽  
Alexa R. Geltzeiler ◽  
Manpreet S. Katari
Keyword(s):  
Genome Viewer

Exploring genomes with a game engine

2014 ◽  
Vol 169 ◽  
pp. 443-453 ◽  
Author(s):  
Jeremiah J. Shepherd ◽  
Lingxi Zhou ◽  
William Arndt ◽  
Yan Zhang ◽  
W. Jim Zheng ◽  
...  
Keyword(s):  
Real Time ◽  
Video Game ◽  
Linear Structure ◽  
Structural Data ◽  
Game Engine ◽  
3D Genome ◽  
Genome Viewer ◽  
A Genome ◽  
Visualization Techniques ◽  
Insight Into

More and more evidence indicates that the 3D conformation of eukaryotic genomes is a critical part of genome function. However, due to the lack of accurate and reliable 3D genome structural data, this information is largely ignored and most of these studies have to use information systems that view the DNA in a linear structure. Visualizing genomes in real time 3D can give researchers more insight, but this is fraught with hardware limitations since each element contains vast amounts of information that cannot be processed on the fly. Using a game engine and sophisticated video game visualization techniques enables us to construct a multi-platform real-time 3D genome viewer. The game engine-based viewer achieves much better rendering speed and can handle much larger amounts of data compared to our previous implementation using OpenGL. Combining this viewer with 3D genome models from experimental data could provide unprecedented opportunities to gain insight into the conformation–function relationships of a genome.

scholarly journals A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database

2020 ◽  
Vol 49 (D1) ◽  
pp. D1496-D1501
Author(s):  
Anne V Brown ◽  
Shawn I Conners ◽  
Wei Huang ◽  
Andrew P Wilkey ◽  
David Grant ◽  
...  
Keyword(s):  
Soybean Genome ◽  
Genetic Maps ◽  
Pedigree Information ◽  
Data Sets ◽  
Visualization System ◽  
Interactive Tools ◽  
Genome Viewer ◽  
Reference Quality ◽  
Soybean Genetics ◽  
Genome Assemblies

Abstract SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensive variant and genotyping data sets. SoyBase displays include genetic, genomic, and epigenetic maps of the soybean genome. Gene expression data is presented in the genome viewer as heat maps and pictorial and tabular displays in gene report pages. Millions of sequence variants have been added, representing variations across various collections of cultivars. This variant data is explorable using new interactive tools to visualize the distribution of those variants across the genome, between selected accessions. SoyBase holds several reference-quality soybean genome assemblies, accessible via various query tools and browsers, including a new visualization system for exploring the soybean pan-genome. SoyBase also serves as a nexus of announcements pertinent to the greater soybean research community. The database also includes a soybean-specific anatomic and biochemical trait ontology. The database can be accessed at https://soybase.org.

scholarly journals MIG: Multi-Image Genome viewer

2013 ◽  
Vol 29 (19) ◽  
pp. 2477-2478 ◽  
Author(s):  
S. J. McGowan ◽  
J. R. Hughes ◽  
Z.-P. Han ◽  
S. Taylor
Keyword(s):  
Genome Viewer

Development of genome viewer (Web Omics Viewer) for managing databases of cucumber genome

2012 ◽  
Author(s):  
M. Wojcieszek ◽  
P. Róż ◽  
M. Pawełkowicz ◽  
R. Nowak ◽  
Z. Przybecki
Keyword(s):  
Genome Viewer ◽  
Cucumber Genome

scholarly journals Chromatic: WebAssembly-Based Cancer Genome Viewer

2018 ◽  
Vol 17 ◽  
pp. 117693511877197 ◽  
Author(s):  
Richard Finney ◽  
Daoud Meerzaman
Keyword(s):  
Ease Of Use ◽  
Data Sets ◽  
Web Browsers ◽  
Web Browser ◽  
Cancer Data ◽  
Genomic Variations ◽  
Genome Viewer ◽  
Code Format ◽  
Generation Sequencing ◽  
Cancer Bioinformatics

Chromatic is a novel web-browser tool that enables researchers to visually inspect genomic variations identified through next-generation sequencing of cancer data sets to determine whether such calls are, in fact, valid. It is the first cancer bioinformatics tool developed using WebAssembly technology, which comprises a portable, low-level byte code format that provides for the rapid execution of programs within supported web browsers. It has been designed expressly for ease of use by scientists without extensive expertise in bioinformatics.

scholarly journals The EcoCyc Database in 2021

2021 ◽  
Vol 12 ◽  
Author(s):  
Ingrid M. Keseler ◽  
Socorro Gama-Castro ◽  
Amanda Mackie ◽  
Richard Billington ◽  
César Bonavides-Martínez ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Regulation Of Gene Expression ◽  
Model Organism ◽  
Web Interface ◽  
Model Organism Database ◽  
Manual Curation ◽  
Genome Viewer ◽  
User Access ◽  
Visualization Tools ◽  
K 12

The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

scholarly journals Chromosome Visualization Tool: A Whole Genome Viewer

2011 ◽  
Vol 2011 ◽  
pp. 1-4 ◽  
Author(s):  
Ethalinda K. S. Cannon ◽  
Steven B. Cannon
Keyword(s):  
Genome Sequencing ◽  
Base Pair ◽  
Visualization Tool ◽  
Whole Genome ◽  
Linkage Groups ◽  
Unit System ◽  
Genome Viewer ◽  
Syntenic Regions

CViT (chromosome visualization tool) is a Perl utility for quickly generating images of features on a whole genome at once. It reads GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features on those chromosomes. It can display features on any chromosomal unit system, including genetic (centimorgan), cytological (centiMcClintock), and DNA unit (base-pair) coordinates. CViT has been used to track sequencing progress (status of genome sequencing, location and number of gaps), to visualize BLAST hits on a whole genome view, to associate maps with one another, to locate regions of repeat densities to display syntenic regions, and to visualize centromeres and knobs on chromosomes.

scholarly journals Visualization for genomics: the Microbial Genome Viewer

2004 ◽  
Vol 20 (11) ◽  
pp. 1812-1814 ◽  
Author(s):  
R. Kerkhoven ◽  
F. H. J. van Enckevort ◽  
J. Boekhorst ◽  
D. Molenaar ◽  
R. J. Siezen
Keyword(s):  
Microbial Genome ◽  
Genome Viewer

scholarly journals Multiple genome viewer (MGV): a new tool for visualization and comparison of multiple annotated genomes

2021 ◽  
Author(s):  
Joel E. Richardson ◽  
Richard M. Baldarelli ◽  
Carol J. Bult
Keyword(s):  
Comparative Genomics ◽  
Inbred Mouse ◽  
Mouse Genetics ◽  
Mouse Strains ◽  
Inbred Mouse Strains ◽  
Multiple Genome ◽  
Link Type ◽  
Genome Viewer ◽  
Genome Features ◽  
Genome Annotations

AbstractThe assembled and annotated genomes for 16 inbred mouse strains (Lilue et al., Nat Genet 50:1574–1583, 2018) and two wild-derived strains (CAROLI/EiJ and PAHARI/EiJ) (Thybert et al., Genome Res 28:448–459, 2018) are valuable resources for mouse genetics and comparative genomics. We developed the multiple genome viewer (MGV; http://www.informatics.jax.org/mgv) to support visualization, exploration, and comparison of genome annotations within and across these genomes. MGV displays chromosomal regions of user-selected genomes as horizontal tracks. Equivalent features across the genome tracks are highlighted using vertical ‘swim lane’ connectors. Navigation across the genomes is synchronized as a researcher uses the scroll and zoom functions. Researchers can generate custom sets of genes and other genome features to be displayed in MGV by entering genome coordinates, function, phenotype, disease, and/or pathway terms. MGV was developed to be genome agnostic and can be used to display homologous features across genomes of different organisms.

scholarly journals pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data

2016 ◽  
Author(s):  
Dan Vanderkam ◽  
B. Arman Aksoy ◽  
Isaac Hodes ◽  
Jaclyn Perrone ◽  
Jeffrey Hammerbacher
Keyword(s):  
Web Applications ◽  
Genomic Data ◽  
Genomic Variants ◽  
Genome Viewer ◽  
Recent Developments

pileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library.

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