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Ethalinda Cannon

CViT - Chromosome Viewing Tool

A collection of Perl scripts that enable quick visualizations of features on genetic sequence. Although primarily developed for whole genome visualizations, CViT can be used to display just about any sort of feature on a stretch of DNA, linkage group, or cytological chromosome. It can handle coordinates in base-pairs, centiMorgans, centiMcClintok, et cetera. Coordinates can be postive or negative, displayed in ascending or descending order.

Uses include display of CGH data, genetic and cytogenetic maps, gene densities, syntenic chromosomal regions, chromosome structure (telomeres, centromeres, pericentromeres, heterchromatic regions).

Input data is one or more files containing GFF3 data. The output is either a PNG or SVG image. (SVG supported added in version 1.1)

Documentation

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Gene models for maize genome assembly B73 RefGen_v2
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BACs, hit densities, CGH, cytogenetic markers


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