GenomeView

Understanding the image

CoGe's genomic visualization library, GeLo, permits the creation of a virtual chromosome using any style of glyphs to represent genomic information. Below are the common implementations used in CoGe

Genomic Features

Genomic features are usually drawn as arrows or blocks of varying size and color. While there is some variation in how such features are drawn due to difference in how they were specified in the original data source (e.g. do mRNAs include introns?), the general conventions used in CoGe are:

• Grey (narrow): Gene. Usually starting at the beginning of the transcript, stopping at the end of the transcript, and including all intronic sequence, if appropriate.
• blue: mRNA transcript
• Green: CDS/protein coding regions (Please see note below)
• grey (large): RNA gene (tRNA, rRNA, etc.)
• orange-red: pseudogene

Note: There are options in CoGe to color protein coding regions (CDS) based on the GC content of the wobble position in the codon. If this visualization is use, a color gradient is used to depict the wobble GC content such that:

• red: AT rich in CDS wobble positions
• green: GC rich in CDS wobble positions
• yellow: 50%/50% AT/GC in CDS wobble positions

background

The background of a genomic image can also be colored. Most often, this is used to color the genomic GC content such that:

• green: GC rich
• white: AT rich