NCBI Genome Data Viewer
The NCBI Genome Data Viewer (GDV) is a genome browser supporting the exploration and analysis of annotated eukaryotic genome assemblies. The GDV browser can visualize different types of molecular data in a whole genome context, including gene annotation, BLAST alignments, and experimental study data from the NCBI GEO and dbGaP databases. GDV release notes describe new features relating to this browser.
The core component of the GDV browser is the NCBI Sequence Viewer, which supports analysis of genomic assemblies at multiple levels, from the whole chromosome or scaffold to the sequence base bair. Please refer to Sequence Viewer documentation and release notes for more information.
Go to the GDV YouTube playlist to view video tutorials that can help you better use this application in your work.
- Finding organisms and genome assemblies
- Using the browser
- Page widgets
- Controlling GDV with URL Parameters
- Cite Us
Finding Organisms and Genome Assemblies
The GDV home page (Figure 1A) offers easy access to the organisms and assemblies represented in the GDV browser. You can enter text into the box on the left side of the page (common or scientific names for organisms and/or taxonomic groupings), or click on nodes in the tree located below this box to explore availabilty. Hovering over tree nodes with '+' signs will open a tooltip that reveals the number of additional nodes with assembly data. Clicking on these nodes will zoom the tree to the next deeper level. To return to the top level tree after zooming in, click the '<<' icon. To go up one taxonomic rank instead, click the '<' icon. Clicking on any of the organism-specific nodes will update the information panel on the right side of the page with information pertaining to the assembly or assemblies that is available in the browser.
Figure 1A: Default (tree) view of the GDV home page used to browse and search genomes and select assemblies to view in the genome browser.
The panel on the right side has a box where users can search for genomic locations in the selected assembly. The Search box accepts search terms such as Genes, dbSNP ids, phenotypes, assembly components/scaffolds, or sequence accessions. Examples of searches relevant to the selected organism are shown below the box to assist you in constructing queries. You can provide location information as a range, point, or cytogenetic band. Results for gene searches with exact matches, as well as location searches, are directed immediately to the genome browser. For more information on browser searches, see the Search section of this document.
If you don't wish to perform a genome search, use the "Browse genome" button to go to a default location, typically the whole molecule view of the first chromosome for chromosome-level assemblies or the longest scaffold for scaffold-level assemblies. Click the "BLAST genome" button to be taken to the NCBI BLAST database page for a genome-specific BLAST. Other links in this panel take you to the annotation report and the NCBI Datasets for the selected organism, where you can download assembly sequences or RefSeq annotations. Click in the ideogram display at the bottom of the panel (available only for organisms with chromosome-level assemblies) to go to the corresponding chromosome in the genome browser.
Figure 1B: Table view of the GDV home page used to browse and select assemblies.
The GDV home page also offers an alternate table configuration (Figure 1B). Here, users can browse through a table of all the assemblies in a taxonomic grouping sorted by species. This view may be helpful for selecting an assembly of interest based on assembly name, assembly level (scaffold vs chromosome), annotation release number, or annotation date. The table contains options to go to NCBI BLAST or NCBI Datasets download services for a selected organism. You can also obtain the annotation report or go to the genome browser view for a selected assembly of interest. Clicking on the "magnifying" glass icon opens an details panel (Figure 1C) with additional options, including the option to searching within a selected genome assembly or navigate to a chromosome in the assembly (if available).
Figure 1C: Table view showing details panel for a selected assembly in the table.
The horizonal tree diagram above top of the table allows you to browse up the taxonomic tree. On the upper right, there's a link to NCBI Datasets to download from any or all organisms in the current table view. You can return to the tree view from this page at any time via the button on the upper left of the page.
Using the Browser
GDV is comprised of a series of page elements (widgets) that are used for different types of interactions with the browser, such as genome searches, analysis of BLAST results, data uploads, or changing the display. The widgets communicate with one another such that an action in one widget causes other widgets on the page to update. For instance, clicking on a chromosome in the Ideogram View will update all other widgets on the page to show information relevant to that chromosome.
An announcement banner appears along the top of the browser page above all the widgets. This banner is updated periodically. Clicking the x on the right end of the banner will remove it from the GDV session. The banner will reappear when the user clicks "Reset All", arrives at a fresh session of GDV, or when the banner message has been updated.
The following links are available in the upper right of the browser header:
- Home: Go to the GDV landing page. Clicking on the "Genome Data Viewer" text on the upper left will also direct you to the landing page.
- Share this page: Generate a temporary URL (90 days) to GDV with current track and display settings
- Reset All: Reset all settings in the browser to default settings
- More Info: Menu with additional options
Below is an overview of GDV that highlights each of the main page elements (Figure 2A). The left sidebar contains a series of widgets that provide tools that can be used to manupulate the display. The center of the page contains an instance of the NCBI Sequence Viewer where tracks and track data is visualized.
This GDV browser view can be customized in several ways. The caret arrow can be used to show or minimize each of the widgets on the left sidebar. These widgets can also be re-ordered by pressing within the header to select, and then dragging and dropping the widget into a desired location in the sidebar.
The entire left sidebar can be hidden by clicking on the blue << icon or by pressing "[" on the keyboard (Figure 2B and Figure 2C). Clicking the >> icon or pressing "[" again will reveal the left sidebar options once again.
Figure 2A: A page overview with individual page elements highlighted in different colors.
Figure 2B: A page overview with the left sidebar hidden and page elements highlighted. Note that the search box is in a different position on the upper right.
Figure 2C: Switch Button to hide/reveal the left sidebar.
Below is an overview description of widgets or elements on the page.
Assembly and Chromosome
Figure 3. Assembly and chromosome indicator/selector menu on the top of the browser page.
The Assembly and Chromosome that are viewed in the genome browser are indicated on the top center of the page (Figure 3). The current sequence accession and coordinates appear on the line below.
The Assembly Indicator appears as a dropdown menu when there are multiple assemblies available in GDV. You can use this menu to switch to view a different assembly for the selected organism.
The Chromosome Indicator appears as a drop-down menu that allows you to navigate to different chromosomes or scaffolds within the assembly. For chromosome-level assemblies, the chromosomes in the assembly will be listed in the menu. For assemblies that lack assembled nuclear chromosomes, (e.g. https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk//genome/gdv/browser/genome/?id=GCF_000297895.1), the menu will contain up to the largest 30 scaffolds/contigs by size. The "More..." option at the bottom of the menu links to the NCBI Nucleotide search results page listing all scaffolds for the given assembly.
Chromosomes or scaffolds that have been viewed in a genome browser session (including scaffolds not in the top 30) will be listed in the selection menu under a separate sub-heading for ease of future access. These added scaffolds will disappear from the menu when you click "Reset All" on the upper right or start a new genome browser session.
Figure 4. Search box with search results shown below. This box appears on the upper right of the page when the left sidebar is hidden.
The Search Box (Figure 4) is located on the upper left of the page by default and can be used to find a gene or location within the selected assembly. You can enter a location, a gene name, SNP RS id, phenotype, or disease term (such as 'PTEN' or 'rs13432' or 'diabetes'). Location information can be provided using a coordinate range, a single point, or a cytogenetic band. This search box can also be used to search and navigate to a scaffold or contig within the assembly (e.g. NW_011934491.1). If your search finds an exact and unique match, the Sequence Viewer and other widgets on the page will update to show the location of that match. If you perform a search without a unique match, a new panel will appear with a list of results and their locations. The Ideogram View and Chromosome Region Selector will also be updated to display clickable colored arrowheads indicating the location of search results.
In the search results panel, the Genes tab lists genes matching the search term, while the Other Features tab lists related transcripts or other features. When you click on a row in either tab of the search results, or on the arrowheads in the Ideogram View or Chromosome Region Selector, the Sequence Viewer and other page elements will update to go to that location. You can click on the x to hide the search results panel. Recent search terms will be remembered by default and shown in a pop-up menu when the cursor is placed within the search box.
When the left sidebar is hidden, the search box appears in the upper right of the page. The right search box has identical behavior to the default search box, and recent searches made in both locations can be retrieved from either location.
Figure 5. Pick Assembly Widget.
The Pick Assembly widget (Figure 5) indicates the current genome assembly and annotation context for GDV. This widget appears in the left sidebar when there are multiple assemblies available for an organism. It provides a drop-down menu of available assemblies. Click on the "Switch organism" link to go to the Genome Data Viewer landing page to select from the full list of available organisms and assemblies.
Figure 6. Ideogram View. Green arrowheads indicate locations of genes found in the most recent search in GDV.
The Ideogram View shows the chromosomes in a NCBI-annotated chromosome-based assembly (Figure 6). A green highlight surrounds the current chromosome that is viewed in the display. Clicking on a chromosome will update the Sequence Viewer to the selected chromosome. No chromosome ideograms will be displayed for scaffold- or contig-based assemblies.
The locations of gene(s) or SNP found in the most recent GDV search appear as green or blue arrowheads, respectively, on the chromosomes in this widget. When you hover over a arrowhead, a panel appears with more information. If data is loaded to the BLAST widget, BLAST hits on the assembly will be shown as orange arrowheads. You can click on an arrowhead or within a pop-up panel to navigate to the corresponding location in the Sequence Viewer display.
The Ideogram View widget also provides a count of the non-chromosomal sequences in the assembly. Separate counts are provided for unlocalized/unplaced scaffolds and for alternate loci/patch scaffolds. The View Scaffolds link goes to the NCBI Nucleotide search results page listing all non-chromosome scaffolds. For more information on these types of scaffold sequences, please see the documentation for the NCBI Assembly Model.
Chromosome Region Selector
Figure 7A. Chromosome Region Selector widget.
Figure 7B. Region pop-up information panel.
The Chromosome Region Selector (Figure 7A) is an interactive ideogram that provides context and navigation for the genome browser. The ideogram corresponds to the current chromosome viewed in browser, and the boxed area in blue denotes the region currently shown in the Sequence Viewer. The Chromosome Region Selector widget will automatically update if you navigate or zoom using the Sequence Viewer or other elements on the page.
You can use the Chromosome Region Selector to navigate to a different region in the Sequence Viewer by clicking and dragging within the ideogram to select a different boxed window. You can also select the ends of the blue box with your cursor and adjust the size of the region. Clicking within a chromosome band (if applicable) will create a box around that band and navigate the Sequence Viewer directly to the sequence corresponding to that cytological region.
The locations of search results (gene or SNP), markers set in the Sequence Viewer, or BLAST results from the BLAST widget will appear as colored arrowheads (gene = green, SNP or marker = blue, BLAST = orange) on the ideogram. When you hover over an arrowhead, a panel appears with more information. You can click on an arrowhead or within a pop-up panel to navigate to the corresponding location in the Sequence Viewer display.
A thin line beneath the ideogram shows regions of the chromosome for which there are alternate loci or patch scaffold sequence representations generated by the Genome Research Consortium (GRC). Hovering over any of the red-colored portions of the line will open a region-specific information panel (Figure 7B) containing the region name and coordinates, as well as sequence identifiers for associated alternate loci or patches. Clicking on the region name or RefSeq accession will take you the corresponding region or accession in the Sequence Viewer, while clicking on the GenBank accession will open the GenBank record in the NCBI Nucleotide database. More information about GRC assembly regions can also be found in the Assembly Region Details widget (Figure 7C), which is located by default toward the bottom of the left sidebar.
Refer to this video for a demonstration of how to use the Chromosome Region Selector.
Figure 7C. Assembly Region Details widget.
Figure 8a. Exon navigator.
Figure 8b. Region menu in the Exon navigator contains options for resetting the view around the selected gene.
The Exon Navigator element (Figure 8a) appears as a blue bar below the Chromosome Region Selector widget. This widget contains drop-down selection menus and arrows that allow a user to navigate among neighboring genes, transcripts of a gene, and exons of a transcript. The "Region" link opens a menu (Figure 8b) containing options to configure the padding of the display around the selected gene or trancript. These options are not available when the view is zoomed further out; instead, a warning message appears listing the number of genes annotated on the latest NCBI Genes annotation release in the current display window.
When a single gene is selected, open circles appear toward the right of the Exon Navigator corresponding to the exons of the selected transcript of the selected gene. You can navigate the Sequence Viewer to a particular exon by clicking on a circle in this widget or using the left/right arrows to jump to upsteam or downstream exons. Hovering over an exon circle reveals text showing the exon number (relative to the selected transcript) and coordinates on the chromosome accession. Right-clicking on an exon circle reveals an option to view a pop-up window showing the genomic sequence of the exon in FASTA format. Users can copy text from this window for their own use.
Figure 9. NCBI Sequence Viewer.
The NCBI Sequence Viewer (Figure 9) is an application that provides a linear graphical representation of features annotated or aligned to individual sequence accessions. You can use the pan arrows and zoom slider on the left side of the Sequence Viewer toolbar to navigate within this viewer; changes in the displayed range will be automatically propagated elsewhere in the genome browser, including to the Chromosome Region Selector and the Exon Navigator.
You can access NCBI Primer-BLAST, set markers, download sequence and track data, generate a PDF or SVG image, and more from within the Sequence Viewer toolbar and context menus. The "Tracks" button (in the upper right of the toolbar) allows you to configure the display with tracks provided by NCBI or to add custom tracks and BLAST request IDs.
Additional information on using the Sequence Viewer (which is embedded on many NCBI pages) can be found on the Sequence Viewer documentation home page.
The BLAST widget (Figure 10A) displays information for BLAST queries (blastn, tblastn) aligned to subject sequences belonging to the assembly displayed in GDV.
Figure 10A: Select BLAST RID menu. The menu is automatically populated with recent BLAST searches and allows you to enter an active RID.
To load alignment data, open and choose from the "Select BLAST RID" menu (Figure 10A), which displays the names/RIDs of your recent BLAST searches at NCBI, or enter any active BLAST RID via the same menu. Multiple results can be loaded from this menu; only the results displayed in the widget table will have a check mark next to their name. Click the x next to an alignment result in this menu to remove it from GDV. Note: if you are on the NCBI BLAST pages, look for and click on the “Genome Data Viewer” link found to the right of your BLAST results to open GDV for the corresponding assembly and load results.
Once loaded to the BLAST widget, the graphical display will update to show the corresponding alignment tracks at top. Track names are provided automatically. Two tracks are provided for each RID: “BLAST results for…” and “Cleaned Alignments-BLAST results for…”. The former provides the raw BLAST hits, while the cleaned alignments track presents a summarized view of co-linear, non-overlapping alignments for each query, connected by thin horizontal lines (Figure 10B). This latter view can be particularly useful if you have aligned a cDNA sequence to the genome assembly, as it tends to connect exon hits together.
Figure 10B: Highlighted alignment tracks. The track name is highlighted in yellow when the corresponding option is selected from the Tools menu.
Figure 10C: BLAST Tools menu.
The Tools menu (Figure 10C) offers several BLAST-associated resources and display options. Use “New BLAST” to initiate a new BLAST search of the viewed genome, or “Show BLAST” to open a new view of the selected BLAST results on the NCBI BLAST web pages. Select “Alignment Inspector” to open a more detailed display of alignments (see below for more information). To remove expired BLAST results from all GDV menus and displays, select “Remove Expired Tracks”.
The Options sub-menu offers 3 choices for the display of alignment tracks. If “Only Show Current BLAST Tracks” is selected, the graphical display will only include the alignment tracks corresponding to results loaded to the BLAST widget table. Choosing the “Highlight Current BLAST Tracks” option will add a yellow highlight (Figure 10B) to the track names in the graphical display that correspond to the results loaded to the BLAST widget table. This is particularly useful if the display is not restricted to the current BLAST tracks. The “Update Location” option, which is on by default, causes the graphical display to update location automatically to the location of the alignment selected in the BLAST widget table.
Expand the “Details” option to see more information about the query, and BLAST program and database for the alignment active in the BLAST widget (Figure 10D).
Figure 10D: BLAST widget. The table is populated with alignments from the selected BLAST search.
The table within the BLAST widget (Figure 10D) summarizes alignment data for the selected search. Within the first column of each table row, the query is shown as a thin gray bar in which the portion shaded orange represents the aligned region. Use the table to select specific alignments and update the graphical display. You can expand the vertical height of the table by dragging the icon located at its base.
Alignment results can be sorted by any column, and an “Accessions Menu” accessed at the top right of the table (red circle, Figure 10D) allows you to quickly jump within the table to specific sequence on which alignments are found. Hovering over any table row activates a highlight at the corresponding sequence location in the graphical display. Click one or more rows in the table to select specific alignments. Use the icons above the table or right-click within the table to: (1) zoom the sequence display, (2) set markers for those selections, or (3) filter result by identity.
Once an alignment has been selected within the table, click the left-most icon above the table to toggle the Alignment Inspector display for the corresponding assembly sequence.
Figure 10E: BLAST alignment inspector. The alignment inspector is launched from the BLAST widget.
The BLAST Alignment Inspector (Figure 10E) provides details for alignments located on the currently displayed assembly sequence. It provides a graphical display of the relationship of a query's alignments to the assembly and NCBI's current RefSeq gene annotation. It is launched from within the BLAST widget using the left-most icon above the table or by right-clicking and selecting the option.
As in the BLAST widget table, the “Query” column in each row of the Alignment Inspector shows an aligned portion of the query as a shaded orange region. In the “Hit Overview” column, the genomic coordinates of the aligned region (orange) are shown in relation to a cartoon representing a specific RefSeq transcript. Thick regions of the cartoons indicate exons, thin regions represent introns, and UTRs are shown in light green.
When you place our cursor in the “Hit Overview” column, you will see a red guide line and tool tip for the corresponding genomic coordinates, including exon-specific details. Hovering over any exon or aligned region creates a highlight in the Alignment Inspector column and at the corresponding region of the sequence viewer display in GDV. A single click within any of these highlights in the Alignment Inspector will navigate the GDV display to the locations of specific alignments, genes, transcripts, or exons. Right-click within an exon or aligned region (orange) for a menu for additional zoom options or to copy the alignment coordinates.
You can also navigate directly to a Gene or RefSeq transcript in the graphical display by clicking on its identifier in the Alignment Inspector. Note that hovering over icons within the Exon Navigator also creates corresponding highlights in the Alignment Inspector.
Add Tracks by Accession
Figure 11. Add Tracks widget.
The Add Tracks by Accession widget (Figure 11) accepts GEO, SRR, dbVar, or dbGaP accessions as input. If the accession is associated with an existing track in the NCBI database, that track will be added to the graphical display. Note: The track must refer to the same assembly as the one currently in the display in order to view data.
Configuring the Track Display in the Sequence Viewer
There are many more data tracks available for GDV than are displayed by default. You can also configure the track order and how tracks are displayed. For example, the "Genes, NCBI Homo sapiens Annotation Release 108" track can be configured to merge all transcript/CDS pairs onto a single line, or you can display each transcript and CDS separately (there are other options as well). To change the track configuration, select the "Tracks" menu in the Sequence Viewer toolbar and select the "Configure Tracks" option. This is highlighted in orange in Figure 12. You can also access track configuration settings using the configure gear icon located in the track title tooltip or on the far left of the track.
Figure 12. Sequence viewer header with the 'Tracks' button highlighted in orange.
This will produce a new dialog that you can use to configure the display (Figure 13).
Figure 13. The Track Configuration page dialog.
Under the Tracks tab at the top of this dialog, the tabs at left represent Track Groups (Figure 13, highlighted in orange). By default, when you first open the "Configure Tracks" panel, the Active Tracks track group will be open. This is the set of tracks that are currently shown in the display. You can re-order tracks in this group simply by dragging and dropping the track name in the section of the dialog where tracks are listed (highlighted in blue). To remove a track from the display, simply uncheck the box.
To change how a track is displayed, select the track and then adjust the options in the Track Settings section of the page (highlighted in green). You can find other tracks in the various track group tabs, and select them to add to the display. Once you are done configuring the display, click on the "Configure" button in the lower right hand corner to apply your changes.
NOTE: To configure the display of tracks from Track Hubs, select the "Configure Track Hubs" menu option.
Track Sets and Collections
In addition to the custom display configuration offered by the "Configure Tracks" panel, the "Tracks" menu also provides access to NCBI Recommended Track Sets (Figure 14). Track Sets are pre-configured assortments of tracks that are commonly viewed together when performing various types of analyses. The names of the track sets indicate the type of analysis for which the track combinations are expected to be most useful (Figure 15). While the content of a Track Set is pre-determined, you can still add, remove or re-order the tracks within the display after selecting a Track Set. Any new combinations of NCBI tracks can be saved as a My NCBI Track Collection that you can re-use or share with others.
Figure 14. Menu of NCBI Track Sets.
Figure 15. Tracks in the Gene Support track set for the GRCh38 human genome assembly.
User Data and Track Hubs
The User Data and Track Hubs widget (Figure 16) allows you to add custom tracks for display in the graphical viewer, by either connecting to a track hub, uploading files, or streaming data from remotely-hosted files. Click on the "Options" drop-down menu to access the different ways to add tracks.
A progress bar at the bottom of the widget will indicate the status of the upload or initial connection to a remote data file (Figure 17). If there are sequences in your file that are not part of the assembly displayed in GDV, a red warning icon will appear next to the confirmation message. However, you will still be able to view tracks for sequences in the file that are part of the assembly. Click on the "Details" link in the status message to view warnings or error messages associated with uploading or streaming your custom track data.
Once added, custom tracks or track hubs will appear in the drop-down menu to the left of the Options menu (Figure 18). Selecting a track from this menu reveals additional metadata about the track in the widget. Tracks that are visible in the current display will be bolded. To remove or disconnect from tracks, click on the X to the right of the track name in the drop-down menu.
File uploads, remotely hosted files, and BLAST results can also be managed via the Configure Tracks panel found under the "Tracks" button on the toolbar of the graphical sequence viewer. Files uploaded or connected from the sequence viewer will also appear in the User Data and Track Hubs widget.
If you are logged into your My NCBI account, your custom tracks and track hubs will be available to you in other NCBI Sequence Viewer instances and browsers displaying the same assembly version (e.g. Variation Viewer). Uploaded tracks will expire 60 days after they are last accessed; streamed tracks and track hubs will persist until you remove them.
Figure 16. User Data and Track Hubs widget.
Figure 17. Confirmation messages that appear when a custom track is added. Note that a track is added to the graphical view in both cases.
You can upload files by going to the Upload sub-menu in the Options menu, or by dragging the file into the widget (Figure 16). The following file types are supported: BED, GFF3, GTF, GVF, VCF, HGVS, ASN.1 (text and binary).
Concurrent upload of multiple files is supported. The upload limit is currently 4 GB per file. The file name will be used as the track's display name, unless an (optional) alternate name is provided. Once uploaded, the track will appear in the graphical display with a green title background and (U) designation, and in the drop-down menu of the User Data and Track Hubs widget (bolded if in the current display).
If an uploaded track has discrete features (e.g. SNPs or gene annotations) on the currently displayed sequence, those features will be listed in a paginated table when that track is selected from the drop-down track selection menu (Figure 18). Hovering the mouse over a table row opens a tooltip with feature details. Click on a row to go to the location of that that feature in graphical view. Use the menus below the table for additional table navigation.
Figure 18. User data feature table.
You can enter a RID (request ID) from a BLAST search into the User Data and Track Hubs widget in the Upload sub-menu in the Options menu. The results will appear as an alignment track in the display. To take advantage of the full range of BLAST analysis tools in GDV, however, select or enter the RID into the BLAST widget.
Remote Streaming Files
BAM, tabix VCF, bigBED, and bigWIG files hosted at publicly-accessible remote locations can be streamed for display in GDV. To add these data as tracks, select Add Remote Files from the Options menu, and enter the corresponding URL in the appropriate box. If viewing a BAM or VCF file, an appropriate index file must be available in the same remote location. The file name will be used as the track’s display name, unless an (optional) alternate name is provided.
Once connected, remotely hosted files will appear in the graphical display with a green title background and (R) designation, and will be listed in the drop-down menu of the User Data and Track Hubs widget (bolded if in the current display).
GDV can display content provided in track hubs format. Select Add Track Hubs from the Options menu to access the Track Hubs panel (Figure 19A). If you’ve already added a track hub(s), you can select Configure Track Hubs to go directly to configure options for your hubs.
Figure 19A. Getting started with Track Hubs.
If you know the URL of the track hub, you can enter it directly into the dialog in the Track Hubs panel (Figure 19B). Alternatively, you can search or browse the Track Hub Registry by keyword or data type. Select a search result to connect to the corresponding hub (Figure 20).
Figure 19B. Search/add Track Hubs dialog.
Figure 20. Track Hubs panel showing search results.
A question mark icon on the lower left of the Track Hubs panel takes you to a tab with additional help documentation for this dialog (Figure 20). You can clear your search results by clicking on the circled x icon on the upper right of the panel.
Upon connecting to a hub, the User Data and Track Hubs widget will display summary information for the selected hub (Figure 21). Connected hubs will also be listed in the drop-down menu of the User Data and Track Hubs widget, designated by (H) (Figure 18).
Figure 21. Track Hub summary information in the User Data and Track Hubs widget.
Connecting to a hub will collapse the search result view (Figure 20) in the Track Hubs panel and expand the configuration view (Figure 22). From this interface, you can select tracks for display, configure track display options, and view hub and track metadata. Currently, you will only be able to connect to tracks that are in BAM, tabix VCF, bigWig/multiWig, or bigBED format. To request support for additional file types found in track hubs, click on the Feedback button located on the lower right of the browser page.
Tracks that the track hub provider has suggested for default display can be distinguished by their black font, while non-default tracks will be listed in light red font. Check the box next to one or more track names to connect to the track. A green circle will appear to the right of a track name once GDV has connected to a track. All connected tracks will show the green ball icon, regardless of whether they are visible in the display. If GDV fails to connect to the track, an error message will be shown.
Click on the hamburger icon to the right of track groupings (e.g. composite track, super track) to access the bulk options dialog (Figure 22 inset). This menu allows you to select or unselect all tracks in that grouping that are marked by default by the hub provider. You can also choose to list only default tracks, i.e hide non-default tracks from the menu.
Figure 22. Track Hubs panel configuration view.
Once connected to a track, you can view and adjust display options for that track (Figure 23). The track will be pre-configured with default options. Where possible and available, GDV will use default display options set by the track hub provider. Display options will differ depending on the track data type (e.g. feature, alignment, or graph data).
Figure 23. Track Hubs panel configuration view showing display options for a connected track.
Once tracks are connected and configured for display, click on the "Configure" button in the lower right of the Track Hubs panel to apply changes and view tracks on the graphical display.
To disconnect from a track hub, click the x located at the far right of the hub name, and then click the Configure button in the lower right of the dialog. You can also click the Disconnect button in the User Data and Track Hubs widget. Disconnecting from a hub will also disconnect all tracks from the hub and remove them from the display.
You can also access the Track Hubs panel by selecting the “Configure Track Hubs” option from the Tracks menu in the graphical sequence viewer toolbar.
Controlling GDV with URL Parameters
There are several parameters that can be added to GDV's URL to control the view's position, add markers and specify SNP locations. These are typically used when constructing links to GDV from other web pages. Note that GDV requires specification of an id in the URL.
|id||Identifier (typically accession) from NCBI resource with associated tracks to be displayed in GDV. Required parameter.||Examples:
|assm||assembly (RefSeq accession). Note: Do not use if an assembly accession is used for "id" parameter.||https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/genome/gdv/?id=GSM923418&assm=GCF_000001405.25|
|context||NCBI resource context that defines default tracks displayed. Examples: GEO, genome, SRA.||https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/genome/gdv/?id=GSM923418&assm=GCF_000001405.25&context=GEO|
|chr||chromosome number (1-X) or alternate locus||Can specify any chromosome name or top-level accession, e.g. 'chr=1', 'chr=X', 'chr=MT', 'chr=NC_000002.11'. If the "acc" parameter is not supplied, the selected assembly will be applied. Examples:
|from/to||range start, end (both 1-based)||Used to specify a genomic range of interest. Requires use of the "chr" parameter. Example:
|q||search term (gene, dbSNP id, etc.). Use of this parameter is only encouraged for developers wishing to create links to GDV in which a specific genomic location will be pre-selected for display.||Searches and selects the location of the first search result. Requires explicit specification of assembly in URL. Examples:
<list-of-marker-spec> - comma separated list of <marker-spec>
Creates marker at defined location. Name & color are optional. Region-spec requires an exact match. Use of strings in ranges or positions not supported.
ts=track set Track Sets
The track set name is case insensitive. It may contain a '*' that will act as a wildcard. Use '%20' to denote a space. User-defined track sets stored in a user's MyNCBI account are supported.
Rangwala SH, Kuznetsov A, Ananiev V, Asztalos A, Borodin E, Evgeniev V, Joukov V, Lotov V, Pannu R, Rudnev D, Shkeda A, Weitz EM, Schneider VA. Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV). Genome Res. January 2021 31: 159-169; Published in Advance November 25, 2020, doi:10.1101/gr.266932.120. PMID: 33239395.