Genotype Comparison Visualization Tool (GCViT)

Written by Dr. Anne V. Brown

  • March 25, 2020

GCViT (Genotype Comparison Visualization Tool) is a new tool for whole genome visualization of resequencing or SNP array data. GCViT allows a user to compare two or more accessions and visually identify regions of similarity and difference across the genome. It can be used in a web environment, with pre-loaded genotype files, or as a stand-alone application, with user-supplied genotype data (in the common VCF format). Currently, GCViT instances are available for soybean, peanut, chickpea, and common bean. GCViT extracts the genotype information from the VCF file for the given lines and notes whether or not ...

A Genome Context Viewer (GCV) “Test-Drive”

Written by: Dr. Nevin Young

  • June 25, 2019

I decided to take GCV out for a test-drive to help answer the question, "Are symbiosis genes, clustered together in the Medicago truncatula genome into so-called ‘symbiotic islands’, also conserved, syntenic and co-linear in the genomes of other legume species?” Because the test-drive was so limited in scope, there’s really no way to reach definitive conclusions about symbiotic islands. But the study did provide insights into symbiotic islands, strengths and limitations of GCV – and also the challenges of comparative genomics based on sequence assemblies coming from diverse sources.

Visualizing Genomes: The Chromosome Visualization Tool

Written by: E. Cannon, A. Wilkey and L. Sanderson

  • Feb. 25, 2019

A whole genome view of genomic or genetic features that can can lead to new insights. For example, gene density compared with specific repeat families, regions of higher heterozygosity in mapping populations, and distribution of BLAST hits across a genome assembly are all cases where the researcher could benefit from a genome-wide view.