Finding Hypothetical Proteins and Pseudogenes - A Style Editor Walkthrough

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Introduction

This walkthrough assumes that you have Java installed properly and are able to run GView.

This walkthrough uses the NC_007622.gbk file provided in GView's example data, but can be used with any valid *.gbk file. The assumption is made that the *.gbk file will contain annotated positive and negative stranded CDS features, hypothetical proteins and pseudogenes. While this is not required, the final appearance may differ significantly.

Launching GView

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  • Launch GView by means of direct execution.
  • Select the NC_007622.gbk file by clicking the "Browse" button adjacent to "Sequence Data".
  • Click "Build Map".
  • GView will automatically apply a default style to the sequence data.
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Launching the Style Editor

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  • Launch the style editor by selecting Style >> Style Editor from GView's menu or using the key combination Ctrl + E.

Adding Slots

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  • Add a new slot by right-clicking the "Slots" node and selecting "New Slot".
    • Select "2" and click "OK".
  • Similarly, add another slot.
    • Enter "-2" and click "OK".
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  • Click the Apply button if you would like to view your changes.
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Adding Feature Sets

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  • Add a new set by right-clicking the "Slot 2" node and selecting "New Set".
    • Select "By Type" for the type of set.
    • Select "CDS".
    • Click "Create".
  • Similarly, add a new set to "Slot -2".
    • Select "By Type" for the type of set.
    • Select "gene".
    • Click "Create".
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  • Click the Apply button if you would like to view your changes.

wt_gv_sets_added.png

Customizing Feature Sets

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  • With the "Slot 2" node expanded, click on the "Type "CDS"" node below it and adjust the following properties:
    • Tooltip Text: select "annotation" and then select "product" from the appropriate combo boxes.
    • Feature Effect: select "basic".
    • Color: click the button and select a color of your liking.
wt_cds_changes.png

  • Click the Apply button if you would like to view your changes.
wt_gv_cds_changes.png

  • Similarly, with the "Slot -2" node expanded, click on the "Type "gene"" node below it and adjust the following properties:
    • Tooltip Text: select "location".
    • Feature Effect: select "basic".
    • Color: click the button and select a color of your liking.
wt_gene_changes.png

  • Click the Apply button if you would like to view your changes.

wt_gv_gene_changes.png

Adding Feature Subsets

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  • With the "Slot 2" node expanded, right-click on the "Type "CDS"" and select "New Subset".
    • Select "Annotation Value Contains" for the type of set.
    • Select "product" for the annotation.
    • Enter "hypothetical protein".
    • Click "Create".
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  • With the "Slot -2" node expanded, right-click on the "Type "gene"" and select "New Subset".
    • Select "Has Annotation" for the type of set.
    • Select "pseudo" for the annotation.
    • Click "Create".
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  • Click the Apply button if you would like to view your changes. However, the subsets should automatically acquire the styling attributes of their parent sets and should currently look exactly the same.
wt_gv_gene_changes.png

Distinguishing Sets and Subsets

  • Note: subsets are currently customized exactly the same as sets.
  • Adjust the colors of the parent sets and their subsets in "Slot 2" and "Slot -2" such that they are distinguishable from each other. In this walkthrough, I will be setting the opacity value of the parent sets to be 100 out of 255 and setting the colors of the subsets slightly differently. Otherwise, the styles of parent sets and subsets will appear identically. We want CDS regions with hypothetical protein products to stand out against other CDS regions without hypothetical protein products. The same idea applies for genes and pseudogenes.
wt_set_color_changes.png

  • Click the Apply button if you would like to view your changes.
wt_gv_set_color_changes.png

Customizing Labels

We would like to use labels as a way of providing further visual indication of the presence of hypothetical proteins and pseudogenes. One way this can be achieved is by using labels.

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  • With the "Slot 2", "Type: "CDS"" and ""product" Contains "hypothetical protein"" nodes expanded, select the "Label Style" node directly below ""product" Contains "hypothetical protein"" node and adjust the following properties:
    • Text Color: A color of your choice. This walkthrough will use the same color as the ""product" Contains "hypothetical protein"" node.
    • Label Text: Select "annotation" and then select "product".
    • Show Labels: Check the box.
wt_labels_proteins.png

  • Click the Apply button if you would like to view your changes.
wt_gv_labels_proteins.png

  • Similarly, with the "Slot -2", "Type: "gene"" and "Has Annotation "pseudo"" nodes expanded, select the "Label Style" node directly below "Has Annotation "pseudo"" node and adjust the following properties:
    • Text Color: A color of your choice. This walkthrough will use the same color as the "Has Annotation "pseudo"" node.
    • Label Text: Ensure "location" is selected.
    • Show Labels: Check the box.
wt_labels_genes.png

  • Click the Apply button if you would like to view your changes. However, there should be no visual changes unless you zoom in significantly and observe labels on the inner most slot.
wt_gv_labels_proteins.png

  • We should now disable the labels on "Slot -1" and "Slot 1".
    • With the "Slot 1" and "(Type: "CDS" And Positive)" nodes expanded, select the "Label Style" node directly below "(Type: "CDS" And Positive)" node and uncheck the "Show Labels" option.
    • With the "Slot -1" and "(Type: "CDS" And Negative)" nodes expanded, select the "Label Style" node directly below "(Type: "CDS" And Negative)" node and uncheck the "Show Labels" option.
  • Click the Apply button if you would like to view your changes.
  • With the GView map object, set the zoom to 1600%, the scale to 100% and the position to 0%.
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  • Mouse over the features to observe their tooltip information.
  • Congratulations on completing the walkthrough!

Additional Materials

The following materials may also prove useful:
 
Contact: Aaron Petkau, Eric Marinier, Matthew Stuart-Edwards at gview@phac-aspc.gc.ca