%0 Journal Article
%T Chromosome Visualization Tool: A Whole Genome Viewer
%A Ethalinda K. S. Cannon
%A Steven B. Cannon
%J International Journal of Plant Genomics
%D 2011
%I Hindawi Publishing Corporation
%R 10.1155/2011/373875
%X 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. 1. Introduction Visualizing features on a whole genome (all chromosomes together) can be informative for many reasons: for identifying genome-wide patterns such as gene or repeat densities, for viewing internal duplications or synteny, for assessing clustering of genes or repeats or other features, for comparing chromosomal structures such as centromeres and pericentromeric regions, or for looking for associations between different types of genomic features. Several very capable genome browsers enable visualization of single chromosomes or regions, but few visualization tools have been developed for whole-genome-at-a-time views. We present CViT (chromosome visualization tool), for viewing a wide range of genomic features on an arbitrary set of linear regions¡ªtypically, all of the chromosomes or linkage groups for a genome. CViT is a set of Perl scripts that generate a PNG (portable network graphics) image of features on chromosomes. It can be executed as a standalone Unix command line utility or wrapped in a web page for either static display or as part of an interactive online tool. The characteristics of the output images are highly configurable. A package containing the CViT code itself along with documentation, examples, supporting scripts, and sample web implementations can be freely downloaded from SourceForge at http://sourceforge.net/projects/cvit/. CViT was initially developed to support the Medicago truncatula sequencing project [1] where it was used to display the assembled bacterial artificial chromosomes (BACs) and the status of the sequencing for each BAC. CViT was also wrapped in web pages to create interactive tools: to display BLAST [2] hits on the whole genome (see http://www.medicagohapmap.org/advanced_search_page.php?seq) and to search where BACs of interest are anchored on the pseudomolecules. For other projects, it
%U http://www.hindawi.com/journals/ijpg/2011/373875/