Data Viewer Manual

1 view

Skip to first unread message

Maren Ruminski

unread,

Aug 3, 2024, 3:52:40 PM8/3/24

to inonplanje

The site is secure.
The ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

The NCBI Genome Data Viewer (GDV) is a genome browser supporting the exploration and analysis of annotated eukaryotic genome assemblies. The GDV browser displays biological information mapped to a genome, including gene annotation, variation data, 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 pair. Please refer to Sequence Viewer documentation and release notes for more information.

The GDV home page (Figure 1A) allows you find and select organisms and assemblies available to view in the browser. You can search directly for common or scientific names using the search box, or click on nodes in the tree to explore different taxa. 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 '

Enter gene names, dbSNP ids, phenotypes, assembly components/scaffolds, or sequence accessions into the search box on the assembly information panel. 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. If your search has an exact location match, you will be taken directly to that location in the genome browser; otherwise, you will be shown a search results panel. 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. You can also click on a chromosome ideogram at the bottom of the panel to go to the corresponding chromosome in the genome browser. Other options in this table will take you outside of the Genome Data Viewer to related analysis resources at NCBI, including the Comparative Genome Viewer (CGV), BLAST, and the NCBI Datasets genome table. You can click on the (i) icon to obtain the annotation report for NCBI-annotated assemblies.

The GDV home page also offers an alternate table configuration (Figure 1B). Here, you 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. You can use the Filter assemblies option to limit the organisms and assemblies displayed in the table to RefSeq accessions that contain annotation from NCBI's annotation pipeline.

The table view contains options to go to the NCBI Comparative Genome Viewer (CGV), BLAST, or NCBI Datasets genome table 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 a details panel (Figure 1C) with additional options, including the option to search within a selected genome assembly or navigate to a chromosome in a chromosome-level assembly.

The horizonal tree diagram above the table allows you to browse up the taxonomic tree. On the upper right, there's a link to NCBI Datasets to download genomic sequence and annotation 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.

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 may appear along the top of the browser page above all the widgets. 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.

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 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. =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.

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 RSID, HGVS pattern, Ensembl gene/transcript ID, phenotype, or disease term (such as 'PTEN' or 'rs13432' or 'diabetes'). Location information can be provided using a coordinate range or a single point. 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.

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.

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.