NCBI Genome Data Viewer

The NCBI Genome Data Viewer (GDV) is a genome browser supporting the exploration and analysis of eukaryotic RefSeq genome assemblies. It allows users to visualize different types of sequence-associated data in a genomic context. Genome Data Viewer is also used by different NCBI resources, such as GEO, to display datasets associated with specified experiments or samples in a genome browser context. Release notes are available for each browser version, describing new features and bug fixes. Videos are available on the GDV playlist to help you get started with various browser features.

Finding Organisms and Genome Assemblies

GDV's landing page offers easy access to the expansive range and number of organisms and assemblies represented in the GDV browser. The landing page is shown in Figure 1. 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 knowledge panel on the right side of the page with information pertaining to the assembly or assemblies that is available in the browser.

GDV Landing Page

Figure 1: The GDV landing page, used for assembly selection, genome searches and offering links to BLAST and other resources.

Within the knowledge panel on the right side of the landing page, you can search for genomic locations in the selected assembly. The Search box accepts search terms such as Genes, dbSNP ids, phenotypes 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 browser. For more information on browser searches, see the "Search" portion of the page widgets section in this Help document.

If you don't wish to perform a genome search, use the "Browse genome' button to go to a default location on the specfied assembly. Click the 'BLAST genome' button to perform an assembly-specific BLAST. Other links in the knowledge panel take you to the corresponding record page in the NCBI Assembly resource and FTP sites at which you can download the assembly sequence or RefSeq annotations. Click in the ideogram display at the bottom of the knowledge panel (available only for organisms with chromosome-level assemblies) to go to the corresponding chromosome in GDV.

Using the Browser

GDV is comprised of a series of '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.

Page layout

The following links are available in the browser header:

Page Overview

Below is an overview of GDV that highlights each of the widgets used to control the display. There is a control column on the left and a graphical display on the right. You can customize the look and feel of the control panel to your liking. Use the toggle icon found at the left side of each widget header to collapse or expand the various panels. Re-order the panels by clicking in the headers and dragging and dropping them into their desired location.

GDV Overview

Figure 2: A page overview with individual page widgets highlighted in different colors.

Page Widgets

Below is an overview for each widget on the page.

Pick Assembly

Pick Assembly Widget

Figure 3. Pick Assembly

The Pick Assembly widget indicates the current genome assembly and annotation context for GDV. If the data that has been specified for display in the GDV URL is associated with more than one assembly, the Pick Assembly widget will appear by default at the top of the control panel at the left side of the browser. It provides a user-selectable menu of the relevant assemblies. To select from the complete list of organisms or assemblies for display in GDV, click the 'Genome Data Viewer' link in the upper left of the page to return to the GDV landing page.

Ideogram View

Ideogram View panel

Figure 4. Ideogram View

The Ideogram View (figure 4) provides viewing context. A green highlight surrounds the chromosome displayed on the right side of the page. This panel can also be used for genome navigation. Clicking on a chromosome will make it the selected chromosome and update the rest of the page to show data for this chromosome. After a Search, the locations of the results appear as triangular annotations on the chromosomes (green=gene search result, blue=other search results (e.g. transcripts, proteins)). If data is loaded to the BLAST widget, BLAST hits on the assembly are shown in shades of orange, with the darker shades indicating better BLAST scores.

The panel 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. For more information on these types of scaffold sequences, please see the documentation for the NCBI Assembly Model .

Chromosome Overview

Chromosome Overview

Figure 5A. Chromosome Overview widget.

Region Panel

Figure 5B. Chromosome Overview Region Tooltip.

The Chromosome Overview widget (figure 5A) provides context and navigation for the page. The blue overlay shown on the ideogram image covers the amount of the chromosome shown in the Sequence Viewer (described below). The sides of this box (outside of the dark blue line) can be selected with the mouse and moved to adjust the size of the box. Making the box smaller is the equivalent of 'zooming' in on a region. You can also select the center of the blue box and drag it to another location on the chromosome. If the blue box is small, you can hold down the 'Alt' key to enable dragging of the blue box. If you adjust the location shown in the Sequence Viewer using any other widget on the page, the blue box will adjust to reflect the location. The thin line beneath the ideogram shows regions of the chromosome for which there are alternate loci or patch scaffold sequence representations. Hovering over any of the filled portions of the line will open a region-specific tooltip (figure 5B) containing the region's name and coordinates, as well as the sequence identifiers of associated alternate loci or patches.

Exon Navigator

Exon Navigator widget

Figure 6. Exon navigator

The Exon Navigator is the blue bar located below the Chromosome Overview widget. When a region of sequence is displayed that includes one or more genes, the symbols for those genes are provided in the menu labeled 'Gene'. The transcripts associated with those genes are listed in the corresponding 'Transcript' menu. You can navigate quickly to a gene by clicking on its symbol in this list. When a single gene is selected, you can move up and down the chromosome, one gene at a time, by clicking on the double arrows (circled red above) to the previous gene (left) or next gene (right) of the Gene selector region. Clicking on the 'Region' link opens a menu that you can use to configure how the gene is displayed in the Sequence Viewer.

When a gene is selected, there will be one or more open circles at the right (highlighted in yellow above) representing the exons of the selected transcript. Navigate to a particular exon by clicking on the appropriate circle; move to the upstream or downstream exon by clicking on the appropriate arrow flanking the exon selector.

Sequence Viewer

Sequence Viewer

Figure 7. NCBI Sequence Viewer

This is the NCBI Sequence Viewer (figure 7), which provides graphical representation of features annotated on individual sequences. Access to other NCBI tools (such as Primer BLAST) and the ability to generate a publication-quality PDF of the browser display are also available within this section from the 'Tools' button in the menu bar. The 'Tracks' button (in the upper right corner) allows you to configure the display. Additional information on using the Sequence Viewer (which is embedded on many NCBI pages) can be found here: .

There are also some videos available on the NCBI YouTube channel that can give you a quick introduction to using the Sequence Viewer.

Search Term Examples

Figure 8. Search widget shown with Search Examples

The Search widget (figure 8) accepts a location directive, such as chr1:1,500,000-2,000,000 or a search term (such as 'PTEN' or 'rs13432'). Clicking on the 'Search examples' link opens a menu of acceptable location formats and other supported search term types. Location information can be provided using a range, a single point or a cytogenetic band. If you search for specified coordinates or a gene or variant id with an exact match, the other widgets on the page will update to that location. If you perform a term search without an exact match, a new window will pop up providing a list of results and their locations (figure 9). The 'Genes' tab lists genes matching the search term. The 'Other Features' tab may list transcripts, phenotypes, genomic clones or Sequence Tagged Sites (STS) associated with the search term. Click on a row in either tab of the search results and the rest of the page will update to go to that location. Additionally, the Ideogram View panel shows the genome-wide locations of your search terms.

Example Search Results

Figure 9: Search Results widget. Clicking on a row will update the page to highlight that location.


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.

BLAST track examples

Figure 10B: Highlighted alignment tracks. The track name is highlighted in yellow when the corresponding option is selected from the Tools menu.

BLAST 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 displayed assembly, 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).

BLAST widget with data

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.

BLAST alignment inspector

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 the mouse 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 zoom 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 copy-paste 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

Add Tracks panel

Figure 11. Add Tracks widget

The "Add Tracks" 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 Display

There are many more data tracks available for GDV than are displayed by default. Additionally, you can configure the track order and how certain 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, click on the 'Tracks' button in the Sequence Viewer header and select the "Configure Tracks" option. This is highlighted in orange in figure 12. Sequence Viewer header

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).

Configure Tracks dialog

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 Tracks Configuration page, the 'Active Tracks' track group will be open. This is the set of all tracks 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 available for display and select them for addition in the various track group tabs. Once you are done configuring the display, click on the 'Configure' button in the lower right hand corner to apply these changes.
NOTE: To configure the display of tracks from Track Hubs, select the "Configure Track Hubs" menu option instead.

Track Sets and Collections

In addition to the custom display configuration offered by the Track Configuration page, the 'Tracks' button 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 to best suit your needs. Any new combinations of NCBI tracks can be saved as a My NCBI Track Collection that you can re-use or share with others. At this time, custom tracks cannot be added to My NCBI Track Collections.

For more information about Track Sets and Track Collections, please see the following FAQ and the 'Track Sets' and 'Track Collections' YouTube videos.

Track Sets menu

Figure 14. Menu of NCBI Track Sets

Gene Support Track Set

Figure 15. Tracks in the 'Gene Support' track set for the GRCh38 human genome assembly

Custom Tracks

User Data and Track Hubs

The 'User Data and Track Hubs' widget (figure 16) allows you to add custom tracks for display in the Sequence Viewer alongside NCBI-provided tracks, by either connecting to a track hub, uploading files, or streaming data from remotely-hosted files. To start, expand the Options menu. Uploaded tracks will expire 60 days after they are last touched in the browser; streamed tracks and track hubs will persist until you remove them. If you are logged in with your My NCBI account and uploading/streaming human data, your custom tracks and track hubs will also be available to you in other NCBI browsers displaying the same assembly version as your data (e.g. Variation Viewer or 1000 Genomes Browser).

A progress bar at the bottom of the widget will indicate the status of the upload or initial connection to a remote data file. If validation detects the presence of target sequences in your uploaded or streamed remote file that are not part of the assembly displayed in GDV, those sequences will be reported as errors, but you will still be connected and able to view tracks for all target sequences in the file that are part of the assembly. To see any warning or error messages associated with uploading or streaming your custom track data, click on the "Details" option that will be a part of the status message.

Your Data Widget

Figure 16. User Data/Track Hubs widget

Track Hubs

GDV can display content provided in 'track hubs'. Select "Track Hubs" from the Options menu to access the dialog for connecting to and configuring track hubs (figure 17A). If you know the URL of the track hub to which you want to connect, you can enter it directly into the resulting dialog (figure 17B). Alternatively, you can use this dialog to search the 'Track Hub Registry' for hubs containing data of interest. Select a search result to connect to the corresponding hub (figure 18). Upon connection, the "Track Hubs/Your Data" widget will display summary information for the selected hub (figure 19). In addition, connection to a hub will collapse the search result view (figure 18) and expand the track hub configuration view (figure 20). Connected hubs will also be listed in the 'select tracks' drop-down menu of the "User Data and Track Hubs" widget, designated by "(H)" (figure 21B).

Hub Selection

Figure 17A. Getting started with Track Hubs

Hub Search

Figure 17B. Search/Add Track Hubs Dialog

Hub Search Results

Figure 18. Track Hub Search Results View

Hub Summary

Figure 19. Track Hub Summary

Once connected to a hub, you can select tracks for display, configure their display options and find hub and track metadata (figure 20). GDV does not automatically add hub tracks to the display. Tracks that the track hub provider has suggested for default display can be distinguished by their black font. Check the box next to one or more track names to connect to the tracks. A green circle will appear to the right of a track name once GDV has connected to the 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. Once connected, track display options will be shown. At this time, GDV will only display tracks that are in BAM, bigWig or bigBED format. Note: BAM files hosted on HTTPS and FTP are not yet supported. To request support for additional file types found in track hubs, click the "Support Center" link located at the lower right of the browser page.

Once tracks are connected and configured for display, click the "Configure" button in the lower right of the dialog to apply these changes to the GDV 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/Track Hubs widget. Disconnecting from a hub will also disconnect all tracks from the hub and remove them from the display.

You can initiate additional searches of the Track Hub Registry from within the "Configure Track Hubs" dialog by clicking the magnifying glass icon located in the "Connected Hubs" header (figure 20). To clear search results, click the circled "x" located at the far right of the search header (figure 18). The hub track configuration view will be collapsed when viewing search results. To return to the hub track configuration view, click the double chevron icon in the "Connected Hubs" header. To return to the current set of search results, click the double chevron icon again.

You can also access the "Configure Track Hubs" dialog by selecting the "Configure Track Hubs" option from the "Tracks" menu in the Sequence Viewer.

Hub Configuration View

Figure 20. Track Hub Configuration View

Uploading Files

You can upload files by selecting one of the following items from the Options menu: "Add Files", "Add URL" or "Add Text", or by dragging the file into the widget (figure 21A). 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 per-file upload limit is currently 4 GB. The file name will be used as the track's display name, unless an (optional) alternate name is provided. Once uploaded, the files will appear in the graphical display with a green title background and (U) designation, and in the 'select tracks' drop-down menu in this widget (bold if in the current display).

If an uploaded track has discrete features (e.g. SNPs or gene annotations, rather than graphs or alignments) on the currently displayed sequence, you can display those features in a paginated table if you select that track from the "User Data and Track Hubs" drop-down menu (figure 21B). Hovering the mouse over a table row opens a tool-tip with feature details. Click on a row to go to the location of that that feature in Sequence Viewer. Use the menus below the table for additional table naviation. To remove uploaded or remote tracks, select the track from this drop-down menu and then click on the 'minus' icon next to the track name. Note: A selected track will be marked by a check-mark in this menu, regardless of whether it has data suitable for tabular display.

Your Data Options

Figure 21A. Getting started with uploads

Your Data Table

Figure 21B. Your Data feature table

Remote Streaming Files

BAM, bigBED and bigWIG files hosted at remote locations can be streamed for display in GDV. To add these data as tracks, select "Add Remote Track" from the Options menu, and enter the corresponding URL in the display (figure 22). If viewing a BAM file, an index file with the .bai extension must be located at the same location as the BAM file. The file name will be used as the track’s display name, unless an (optional) alternate name is provided. A progress bar will indicate the status of the connection and validation processes. Once connected, remotely hosted files will appear in the graphical display with a green title background to their title and will also be listed in the 'select tracks' drop-down menu of the "User Data and Track Hubs" widget, designated by "(R)" (bold if in current display). Note: BAM files hosted on HTTPS and FTP are not yet supported. To request streaming support for additional file types, click the "Support Center" link located at the lower right of the browser page.

Your Data Remote Options

Figure 22. To add data hosted at remote locations, select "Add Remote File".

BLAST Results

You can also enter the RID from a BLAST search into the User Data and Track Hubs widget. 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.

File uploads, streaming of remotely hosted files and BLAST results can also be managed via the track configuration menu found under the 'Tracks' button at the top right of the Sequence Viewer display. Files uploaded or connected by this mechanism will also appear in the 'Your Data' widget.

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.

Parameter Definition Example
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.
context NCBI resource context that defines default tracks displayed. Examples: GEO, genome, SRA.
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:
  • by RS ID:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&q=rs328
  • by dbVar ID:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&q=nsv531182
  • by gene symbol:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&q=INTS10
  • with Sequence Viewer marker:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&q=ALDH2&mk=112227634|myMarker
  • by gene ID:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&q=55174[geneid]
  • by cytogenetic band:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&q=1q21
  • Note: when using "q" parameter, "from, to" parameters are ignored.

<list-of-marker-spec> - comma separated list of <marker-spec>
where <marker-spec> = position|name|color - the color is optional

Creates marker at defined location. Name & color are optional. Region-spec requires an exact match. Use of strings in ranges or positions not supported.

  • Single marker:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&mk=chr1:74733990-74733996|MyMarker|green
  • Multiple markers:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&chr=1&mk=5000000-505000|MyMarker|green,10000000|RS|80f0c0,15000000|RS2
  • With query term:,GSM923422,GSM923420&context=GEO&assm=GCF_000001405.25&q=ALDH2&mk=112227634|myMarker

Support Center

Last updated: 2018-08-16T13:27:56Z