What is the Genome Decoration Page?

The Genome Decoration Page (GDP) is a service that allows users to upload their own annotation data and create a diagram showing that annotation distributed on the genome. Annotations can be shown as a track, or set of tracks, drawn next to the chromosome. An annotation track can be selected to be drawn as an 'Overlay', such that the annotation information is drawn on top of the chromosome representation. 

How does this work?

Step 1: Select Genome Information

• Select an organism from the pulldown menu. Currently we can support genomes that have a chromosome-level assembly. If you would like to have an organism added, please use the 'Support Center' link at the bottom of the page to make your request. As soon as you select an organism, a preview will be shown. To see how additional selections affect the figure, click the 'Refresh' button at the top of the 'Ideogram Preview' window.
• Select the genome representation you would like. This involves selecting an assembly and an ideogram representation. Choosing 'cytogenetic' means the chromosomes will be rendered with standard banding patterns. The cytogenetic option is only available for a subset of organisms. Choosing 'sequence' means there will be no bands drawn, just a chromosome representation with centromeres (when the data is available). If you choose 'cytogenetic' you can still provide your annotation data in sequence coordinates. Whether you chose 'cytogenetic' or 'sequence', you will still need to select a specific assembly as the cytogenetic to sequence relationship is different in each assembly.
• If you do not want all chromosomes displayed, click the 'selected' button by the 'Chromosomes:' label. This will allow you to select the chromosomes you would like to be displayed in your figure.
• A preview of your images will be shown to the right of the selection menus. As you update the form, click the 'Refresh' button at the top of the image. You can click the 'Refresh' button as often as you would like and you can see how your selections affect the image.

Step 2: Set up your layout

• Define the layout for the figure:
  • Select the font type you would like used in the figure.
  • Define how you would like the chromosomes aligned:
    • Aligned at the top
    • Aligned at the bottom
    • Aligned at the centromere
  • Define whether the chromosomes should be drawn horizontally or vertically.
  • Choose whether the chromosomes should be displayed on a single line or on two lines.
  • You can adjust the size of the chromosomes by typing the size, in pixels, (height and width) by typing the sizes in the text box.
  • Next, define if you would like chromosome labels displayed, and whether they should be displayed before (or on top) or after (or on bottom) of the chromosome.
  • Pick the font size and color for the chromosome labels.
  • If you chose a 'cytogenetic' representation, you can choose whether band labels are displayed and how they are displayed.
  • You can also set up a figure legend if you wish to have one on the page. You can select the position of the legend relative to the chromosomes (below or to the right), or select 'None' if you don't want a figure legend. You can also adjust font size and color as well as text direction.

Step 3: Upload your annotations

Annotations can be displayed on the ideogram images as a track (features drawn beside the chromosome) or as an overlay (features drawn on top of the chromosome representation).

You can only define one file for overlay annotation, but you can add up to 16 files that will be displayed as separate annotation tracks. To add annotations:

• Upload your annotation file.
  • If your annotations are in sequence coordinates, upload a file that is formated in one of the following formats. Note that the seqid column (column 1) must use NCBI RefSeq accessions, e.g. NC_000001.11.
    • GTF
    • GFF
    • GFF3
    • GVF
    • BED
    • HGVS
  • If your annotations are in cytogenetic coordinates you can just upload a list of the cytogentic locations; for example:
    1q21
    1q21-q22
• Choose the color and shape you would like to use for your annotations.
• Select the width of the annotation track. 
• Provide a 'Track name' for use in the figure legend. 
• To add additional tracks, select the 'Add track' button and repeat Annotations steps 1-4.
• The 'Advanced formatting' link allows you to apply custom rendering to specific features in your file based on one or more attributes of interest.
  • Currently, this only works with the text in the ID field value found in column 9 of GFF3 annotation files.
  • If you would like us to extend this capability, please use the 'Support Center' link at the bottom of the page. 

Note: If the upload function cannot read your file, you will be notified via an alert. If the file is read properly, but there are sequence locations in the file that the process doesn't know how to interpret you will be given a list of warnings below the ideogram preview. These warnings will not show up until you hit the 'Refresh' button. If you have loaded multiple files, the warnings within each file will be listed with a header denoting where the warning list for each file begins. 

Step 4: Download your file

Once the ideogram figure is set up the way you would like, you can download the file in the following formats:

• png
• jpeg
• tiff
• eps
• svg
• pdf

Note: If you have trouble with an HGVS expression, please use the 'Write to Help Desk' link at the bottom of the page and report the expression to us so we can improve our parser.

Last updated: 2017-03-09T10:46:23-05:00