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:
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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.
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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.
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3. The next stage provides the researcher with the ability to customize their BLAST parameters.
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4. The next stage provides the researcher with the ability to customize how the results of the analysis are displayed.
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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.
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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.
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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.
- 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
or 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
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
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
- Core Genome
A Core Genome analysis can be used to identify regions within the reference genome which exist in all the query genomes.
Process:
Step 1 - Choose Analysis and Upload Reference
- Select Core genome 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 a sequence database file. The sequence database file should contain one or more genomes in FASTA format (i.e. one genome per fasta entry) or GenBank format
- Click show advance settings to choose the direction of BLAST (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 reference genome file (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
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
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 core genome may be viewed by selecting 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: Core Analysis
- Accessory Genome
The Accessory Genome analysis can be used to display regions found within the reference and query files, but not within the core genome. More specifically, the accessory genome of closely related genomes consists of regions found in at least two genomes (must be in the reference and at least one query genome) but not in all genomes.
Process:
Step 1 - Choose Analysis and Upload Reference
- Select Accessory genome 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 a sequence database file. The sequence database file should contain two or more genomes in FASTA format (i.e. one genome per fasta entry) or GenBank format
- Click show advance settings to choose the direction of BLAST (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 reference genome file (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
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
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 Accessory genome may be viewed by selecting 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: Accessory Analysis
- Unique Genome
The Unique Genome analysis can be used to display regions unique to the reference genome. More specifically, the unique genome consists of regions in the reference genome not found in the query genomes.
Process:
Step 1 - Choose Analysis and Upload Reference
- Select Unique genome 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 a sequence database file. The sequence database file should contain two or more genomes in FASTA format (i.e. one genome per fasta entry) or GenBank format
- Click show advance settings to choose the direction of BLAST (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 reference genome file (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
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
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 Unique genome may be viewed by selecting 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: Unique Analysis
- Signature Genes
The Signature Genes analysis can be used to display genes which are unique to the inclusion genome group in comparison to the exclusion genome group. That is, signature genes are those present in the reference and the inclusion group, but not in the exclusion group.
Process:
Step 1 - Choose Analysis and Upload Reference
- Select Signature genes 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 the inclusion genomes file. The inclusion file should contain one or more genomes in FASTA format (i.e. one genome per fasta entry) or GenBank format
- Upload the exclusion genomes file. The exclusion file should contain one or more genomes in FASTA format (i.e. one genome per fasta entry) or GenBank format
- Click show advance settings to choose the direction of BLAST (i.e. BLAST query genome(s) to reference genome or vice versa)
- Click Continue
Step 3 - BLAST Parameters
- Select the BLAST program to use for each genome group. 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 reference genome file (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
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
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 signature genes analysis may be viewed by selecting 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: Signature Analysis
- Pangenome Analysis
The Pangenome Analysis can be used to describe the full complement of genes within a group of closely related genomes. A pangenome will be constructed based upon all of the uploaded genomes. The pangenome will be used as the reference for a BLAST Atlas. This makes sure that we include all genomic content in our analysis, not just regions found within the reference.
Process:
Step 1 - Choose Analysis
- Select Pangenome Analysis as the analysis type. There is no reference file to upload.
- Optional: enter your email address to receive an email with a link to your results upon completion
- Click Continue
Step 2 - Upload Query File
- Upload two or more genome files to be used in the pangenome analysis. Accepted formats are GenBank, EMBL, and FASTA. At least one of the genomes must be in a GenBank or EMBL format. To add or remove genomes click on
or .
- Click Continue
Step 3 - BLAST Parameters
- For each genome, select which BLAST program to use. The options will be restricted based on the data in the uploaded files.
- For each genome, select the genome sequence or features to be used in the BLAST analysis
- While loading your genome files, GView server will identify available features within your reference genome file (i.e. CDS, rRNA, tRNA, gene)
- Note: selecting both CDS and gene can yield duplicate results!
- Identify which genome will be used as the seed genome to build the pangenome.
- 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
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
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 Pangenome Analysis may be viewed by selecting 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: Pangenome Analysis
- Reciprocal BLAST
The Reciprocal BLAST analysis can be used to identify orthologous regions between two genomes.
Process:
Step 1 - Choose Analysis and Upload Reference
- Select Reciprocal BLAST 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 File
- Upload a query genome to BLAST against the reference genome. Accepted formats are GenBank, EMBL.
- Click Continue
Step 3 - BLAST Parameters
- Select which BLAST program to use against the reference. The options will be restricted based on the data in the uploaded files.
- Select which BLAST program to use against the query. 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 reference genome file (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
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
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 Reciprocal BLAST results may be viewed by selecting 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: Reciprocal analysis
- Custom Analysis
A Custom analysis can be used to create a custom BLAST analysis or custom GView image. For example, a custom analysis can be created with slots illustrating results from various analysis types (i.e. core genome in one slot, accessory genome in another slot).
Alternatively, a custom analysis type can be created using BLAST Logic operators where the user can perform customized logical operations on one or more genomes. The Custom BLAST Logic is for advanced BLAST users. For more information, please refer to the following document: Blast logic.pdf.
Process:
Step 1 - Choose Analysis and Upload Reference
- Select Custom analysis 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 - Global BLAST Settings
- Select the Reference genome split size. The custom BLAST analysis will split the reference genome into segments to BLAST against the query. The user can adjust the segment size to ensure that similar blocks of interest are not split.
- Select a Reference genome split overlap size. The split overlap size refers to the number of bases to overlap between segments. Setting an overlap will ensure that similarity blocks near segment junctions are not truncated or overlooked.
- Choose the direction of BLAST (i.e. BLAST query genome(s) to reference genome or vice versa)
Step 3 - Track/slot analysis settings
- Click on show advanced BLAST settings link to expand BLAST parameter options.
- Select the analysis type for a track/slot and set BLAST parameters to use. For more information regarding an analysis type, please refer to the documentation for that particular analysis. For more information regarding BLAST Logic, please refer to the following document: Blast logic.pdf.
- To add another slot/track click Add Another Track and repeat previous step.
- When all tracks/slots have been added and the analysis parameters defined, 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
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
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 Custom analysis results may be viewed by selecting 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
Appearance 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 Title | This sets the title to be displayed on the GView Map. |
Description | This 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 features | This controls which regions on the reference genome to display when creating the resulting images. |
Show GC Content | This controls whether or not to show a plot of GC Content on the reference sequence. |
Show GC Skew | This controls whether or not to show a plot of the GC Skew on the reference sequence. |
Show COG Categories | This 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 Legends | This option defines whether or not to show a legend of the data on the map. |
Select a font | This 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 is used to split the slots, and the 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 Colour | The colour to draw the displayed features within this slot. |
Thickness | The thickness of the features as a proportion of the slot size. |
Slot Size | The size of the slot containing the features. |
Feature Shape | The shape to draw the features within this slot. |
Feature Effect | The effect to apply to the feature shapes. |
Tooltip Text | The text to use for the tooltip/mouseover. This will be taken from the appropriate field in the sequence file. |
Show Slot Labels | Whether or not to show labels for the features in this slot. |
Label Text | The 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 Colour | The colour of the backbone element. |
Thickness | The 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 1 | Colour to use for the GC content above the average. |
Use Two Colours | Whether or not to use two colours for the GC content plot. |
GC Content Colour 2 | colour to use for the GC content below the average. Only applicable if Use Two Colours is selected. |
Grid Colour | Colour to use for the grid lines in the GC content plot. |
Slot Size | Size of the GC content slot. |
Grid Lines | Number 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 1 | Colour to use for the GC skew above the average. |
Use Two Colours | Whether or not to use two colours for the GC skew plot. |
GC Skew Colour 2 | Colour to use for the GC skew below the average. Only applicable if Use Two Colours is selected. |
Grid Colour | Colour to use for the grid lines in the GC skew plot. |
Slot Size | Size of the slot for the GC skew plot. |
Grid Lines | Number 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.