Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)

Abstract

The National Center for Biotechnology Information (NCBI) is an archive providing free access to a wide range and large volume of biological sequence data and literature. Staff scientists at NCBI analyze user-submitted data in the archive, producing gene and SNP annotation and generating sequence alignment tools. NCBI's flagship genome browser, Genome Data Viewer (GDV), displays our in-house RefSeq annotation; is integrated with other NCBI resources such as Gene, dbGaP, and BLAST; and provides a platform for customized analysis and visualization. Here, we describe how members of the biomedical research community can use GDV and the related NCBI Sequence Viewer (SV) to access, analyze, and disseminate NCBI and custom biomedical sequence data. In addition, we report how users can add SV to their own web pages to create a custom graphical sequence display without the need for infrastructure investments or back-end deployments.

Figure 1.

NCBI Sequence Viewer (SV) is the graphical component of many NCBI pages and is configured to display data appropriate to the resource page. (A) SV located on an NCBI gene record page. Brown labels indicate tracks for sequence, gene annotation, and RNA-seq data. (B) SV located on an NCBI SNP record page. Brown labels indicate tracks for gene annotation, RefSNPs, Clinical (ClinVar), missense, and frameshift variants. A marker is automatically placed over the variant described on the page.

Figure 2.

Genome Data Viewer (GDV) home page (https://www.ncbi.nlm.nih.gov/genome/gdv/). Users can search for an organism (A) or browse the taxonomic tree (B). There is also an option to navigate the available genome assemblies in table form (C). The panel on the right side provides information and links for the selected assembly. Adding a location or gene symbol in the search box (D), clicking on the “browse genome” button (E), or clicking on a chromosome in the ideogram (F) will take the user directly to the genome browser view. There are also options to BLAST the genome (G), download information using the NCBI Datasets interface (H), and obtain information about the annotation (I).

Figure 3.

GDV. (A) NCBI SV embedded application; (B) search box; (C) region selector ideogram; (D) exon navigator; (E) zoom and pan options from SV; (F) tracks configuration menu from SV to add NCBI-provided tracks; (G) user data and track hubs and BLAST widgets to add custom tracks; (H) download data options from SV; (I) buttons to download track data, change track settings, or hide tracks (x); (J) share this page link; and (K) news banner.

Figure 4.

Tracks supplied by NCBI can be added using the track configuration panel (A), which can be accessed from the tracks menu located in the SV toolbar. The tracks menu on the toolbar also provides the option to add predetermined sets of tracks from the NCBI recommended track sets menu (B) or private track sets saved in “My NCBI Track Collections” (C). Track display settings can be changed within the track configuration panel (D).

Figure 5.

Track data displays for different track types. (A) Gene annotation track showing two transcript variants in a gene selected using mouse clicks. Green indicates gene; purple, transcript; red, coding sequence (CDS). Red hairlines denote positions where the transcript variants show differences in splicing. (B) MultiWig files displayed as overlay (top) or stacked (bottom set) graphs. (C) Pile-up graphs and tables for alignment data, for example, BAM files. (D) Example of data available in the tooltip of an alignment, along with a pop-up view showing sequence of unaligned nucleotides.

Figure 6.

GDV session displaying the BLAST Alignment Inspector. When the cursor hovers over an aligned region in the BLAST Alignment Inspector (A), the corresponding region in the SV is highlighted as well. Note the full list of alignments is reported in a table in the BLAST panel (B). BLAST alignments can also be viewed as tracks added to the SV (C).

Figure 7.

Organization of data flow for SV to NCBI in-house tools (such as the NCBI GDV browser) and non-NCBI web pages. Both GDV and non-NCBI web pages communicate with the NCBI back-end to obtain sequence and annotation data hosted at NCBI. Non-NCBI streaming data must also access NCBI back-end servers in order to be displayed in the NCBI graphical viewer application.