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United States Department of Agriculture

Agricultural Research Service

Research Project: CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES

Location: Corn Insects and Crop Genetics Research

Title: CViT: “Chromosome Visualization Tool” – A whole-genome viewer

Authors
item Cannon, Ethalinda -
item Cannon, Steven

Submitted to: International Journal of Plant Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 4, 2011
Publication Date: December 20, 2011
Citation: Cannon, E.K., Cannon, S.B. 2011. CViT: “Chromosome Visualization Tool” – A whole-genome viewer. International Journal of Plant Genomics. DOI:10.1155/2011/373875.

Interpretive Summary: Researchers who study genetics often have a need to visualize information about all of the chromosomes of the organism they study. Such information might be about the relative location of genetic traits on the chromosomes, or the locations of genes or other identifiable features. This paper describes a computer program, "CViT," for visualizing such information for all of the chromosomes (the genome) in an organism. While other software exists for displaying genetic information on single chromosomes at a time, few programs have been written to display the information for entire genomes in a single view. The described computer program has been used so far to present genetic data for corn (at the Maize Genome Database, MaizeGDB; http://maizegdb.org), and for soybean and other species at the Legume Information System (LIS; http://comparative-legumes.org). This software should help researchers and plant breeders track and identify features of importance, and to speed the process of variety improvement.

Technical Abstract: CViT (Chromosome Visualization Tool) is a Perl utility for quickly generating images of features on a whole genome at once. It reads GFF3-format data representing chromosomes (linkage groups or pseudomolecules), and features on those chromosomes. It can display features on any chromosomal unit system, including genetic (centi-morgan), cytological (centi-McClintock), and DNA units (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, and to visualize centromeres and knobs on chromosomes. CViT is freely available on SourceForge: http://sourceforge.net/projects/cvit/.

Last Modified: 7/28/2014
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