Guide

February 9, 2021: Job submission for GView Server is back to normal.

Introduction

GView Server is a comparative genomics server and front end to GView, a circular and linear genome viewer. Support is provided for a number of different types of comparative analyses. Each type of comparative analysis has its own wizard-style interface to guide the researcher through the setup, analysis, and display of the final results of their data.

Most analyses follow the same general procedure:

  • 1. The researcher first selects the type of analysis to perform and uploads a reference genome file. The reference genome file is used as the starting point for the remaining analysis. The one exception is the pangenome analysis, where the reference is constructed from a set of uploaded genomes.
  • 2. The following stage prompts the researcher to upload one or more additional sequences for comparison to the reference. Additional options are provided to customize each analysis.
  • 3. The next stage provides the researcher with the ability to customize their BLAST parameters.
  • 4. The next stage provides the researcher with the ability to customize how the results of the analysis are displayed.
  • 5. Following this, the analysis job is submitted to GView Server and the researcher is provided with a unique job id and URL that can be used to check on the status of the submission.
  • 6. On completion, the researcher is presented with the results in the form of a genome map. Static circular and linear images are provided, or the results can be launched in GView. A table of the results of the BLAST analysis is also provided.
Choose Analysis Upload Files BLAST Setting Appearance Settings Submission Results
1: Choose Analysis 2: Upload Files 3: BLAST Settings 4: Appearance Settings 5: Submission 6: Results

Analysis Types

Instructions on how to perform each type of analysis as well as an example of the results are given below. Click on any of the below links to open the appropriate section.

  1. Blast Atlas

    Blast atlas is a comparative genomics tool used to compare a reference genome to one or more query genomes. Blast results can be visualized using GView, an interactive genome viewer, or downloaded as an xls or csv file.

    Process:

    Step 1 - Choose Analysis and Upload Reference
    • Select Blast atlas as the analysis type
    • Upload a reference genome file. Accepted file formats are GenBank and EMBL. The file must include the genomic DNA sequence and must consist of a single contig.
    • Optional: enter your email address to receive an email with a link to your results upon completion
    • Click Continue

    Step 2 - Upload Query Files
    • Upload query genome files. Accepted file formats are GenBank, EMBL, or FASTA. Click on plus or minus to add or remove genomes.
    • Click on show advanced settings to adjust the BLAST direction (i.e. BLAST query genome(s) to reference genome or vice versa)
    • Click Continue

    Step 3 - BLAST Parameters
    • Select the BLAST program to use. The options will be restricted based on the data in the uploaded files.
    • Select the genome sequence or features for the reference and query genome(s) to be used in the BLAST analysis
      • While loading your genome files, GView server will identify available features within your files (i.e. CDS, rRNA, tRNA, gene)
      • Note: selecting both CDS and gene can yield duplicate results!
    • Customize your BLAST parameters
    • Click Continue

    Step 4 - Customize and Complete
    • Customize the genome map view (i.e. map title, show COG categories, features to display, GC content and skew, legend, font)
    • Additional customizations:
      • Drag and drop track boxes to re-order them on the GView map
      • Click on the Edit styles icon on one of the track boxes to customize the style for that slot within the genome map (i.e. colour and slot size)
      • Click on the Split positive and negative strands icon within the track boxes to split the slot into positive and negative strands
    • Click Complete

    Final Step - Viewing results
    • a circular or linear version of the Blast Atlas may be viewed by clicking on the preview image
    • Selecting the Webstart links will launch the GView application from the web
    • You may download the standalone GView application, resulting data from the job, and/or BLAST hits table in csv or xls format
    • For a description of the results, please see: BLAST Atlas
  2. Core Genome
  3. Accessory Genome
  4. Unique Genome
  5. Signature Genes
  6. Pangenome Analysis
  7. Reciprocal BLAST
  8. Custom Analysis

Appearance Settings

GView Map Settings

The final stage provides some settings to control the overall appearance of the GView map produced from the uploaded data. The options include:

Map TitleThis sets the title to be displayed on the GView Map.
DescriptionThis sets an optional name for the job which is used for reviewing a user's jobs. This option only exists for a user who is logged in.
Display reference featuresThis controls which regions on the reference genome to display when creating the resulting images.
Show GC ContentThis controls whether or not to show a plot of GC Content on the reference sequence.
Show GC SkewThis controls whether or not to show a plot of the GC Skew on the reference sequence.
Show COG CategoriesThis turns on an additional analysis to show COG categories of CDS regions on the reference sequence. This will be shown in an additional slot above the reference with each colour corresponding to a different COG category.
Show LegendsThis option defines whether or not to show a legend of the data on the map.
Select a fontThis option defines the font used for the labels on the map.

Additional Customizations

In addition to the above it is also possible to customize the style of each individual slot to display on the GView Map. Slots can be dragged and dropped in the order that is desired to display on the map. The Backbone slot defines the center of the map, along which other slots will be displayed, either above or below.

The features to display on each slot can be "split" into two slots displaying the forward and reverse stranded features. The icon Split Icon is used to split the slots, and the icon Join Icon is used to merge the slots back together.

Slot Appearance

The Slot Appearance window allows customization of the style of the features to be displayed in each individual slot. The options include:

Feature ColourThe colour to draw the displayed features within this slot.
ThicknessThe thickness of the features as a proportion of the slot size.
Slot SizeThe size of the slot containing the features.
Feature ShapeThe shape to draw the features within this slot.
Feature EffectThe effect to apply to the feature shapes.
Tooltip TextThe text to use for the tooltip/mouseover. This will be taken from the appropriate field in the sequence file.
Show Slot LabelsWhether or not to show labels for the features in this slot.
Label TextThe text to use for the labels. This will be taken from the appropriate field in the sequence file.

Backbone Style

The Backbone Style window allows customization of the style of the Backbone element on the map. The Backbone element is the element that is used to separate the positive (outer) and negative (inner) slots. The options include:

Backbone ColourThe colour of the backbone element.
ThicknessThe thickness to use for the backbone element.

GC Content

The GC Content window allows customization of the plot used to display the GC Content. The options include:

GC Content Colour 1Colour to use for the GC content above the average.
Use Two ColoursWhether or not to use two colours for the GC content plot.
GC Content Colour 2colour to use for the GC content below the average. Only applicable if Use Two Colours is selected.
Grid ColourColour to use for the grid lines in the GC content plot.
Slot SizeSize of the GC content slot.
Grid LinesNumber of lines to use for the grid in the GC content plot.

GC Skew

The GC Skew window allows customization of the plot used to display the GC Skew. The options include:

GC Skew Colour 1Colour to use for the GC skew above the average.
Use Two ColoursWhether or not to use two colours for the GC skew plot.
GC Skew Colour 2Colour to use for the GC skew below the average. Only applicable if Use Two Colours is selected.
Grid ColourColour to use for the grid lines in the GC skew plot.
Slot SizeSize of the slot for the GC skew plot.
Grid LinesNumber of lines to use for the grid in the GC skew plot.

Viewing Results

The results of any analysis can be viewed through the provided results page. This page contains circular and linear GView images of the analysis, a link to launch the results using GView, and links to download the GView results for later viewing, or download a table of all the BLAST analysis data.

Viewing in GView

GView Server uses GView, a circular and linear genome viewer, to display the results of the analysis. The results may be launched in the GView viewer directly through the provided Java web start links (Webstart - Circular or Webstart - Linear) under the View section. Alternatively, the results and GView executable can be downloaded for viewing offline using the gview-all.zip or gview-data.zip links under the Download section. The standalone results can be launched by running the provided QuickLaunch scripts (QuickLaunch.sh or QuickLaunch.bat). More information on how to use GView can be found in the GView Viewer documentation.

Downloading the BLAST Results

The results from a BLAST analysis can be downloaded in CSV or Excel format using the blast-results.csv or blast-results.xls links in the download section. The table lists the results of the BLAST analysis between the reference and query files that are kept to make up the GView map. One result is listed per line.