GenomeView

Interface to GenomeView

Getting additional information and data=

Annotations

Full Annotations

===Popup-annotations

Understanding the image

Background of chromosome colored green to show GC rich regions

Gene models drawn as gray arrows

mRNA drawn as blue arrows (on top of gray genes)

Protein coding regions (CDS) drawn as green arrows (on top of gray genes and blue mRNAs)

Overlapping genomic features are detected and expanded to show alternatively spiced transcripts

Genomic region with unsequenced regions colored orange from the genome of Carica papaya

Genomic region with masked sequence colored purple

Microbial (archaea) genomic region with 23S and 16S rRNA genes drawn as wide gray arrows

Microbial (archaea) genomic region with many pseudogenes drawn as orange-red arrows

Wobble GC content colored for Chlamydomonas reinhardtii genome. Green means high GC content in codon wobble positions

Wobble GC content colored for Chlamydomonas reinhardtii chloroplast genome. Red means low GC content in codon wobble positions

Wobble GC content colored for Chlamydomonas reinhardtii mitochondria genome. Yellow means ~50% GC content in codon wobble positions

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
• purple: masked sequenced (X). Masked genomes are generated often to remove repetitive sequence.

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 of virtual chromosome

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
• orange: Unsequenced (N)

Expanding overlapping genomic features

When genomic features overlap, as happens with alternatively spliced transcripts, you often have the option of drawn these on top of one another, or have CoGe detect this and drawn them above and below one another.