Genome Data Viewer (GDV) is a browser developed by the National Center for Biotechnology Information (NCBI) for exploring genome assemblies and associated molecular data. It brings together genome annotations, sequence information and experimental results within a coordinated graphical interface.
The application is built around NCBI’s Sequence Viewer, which displays genomic information at different scales. Researchers can examine an entire chromosome, investigate a selected region or inspect individual sequence features without switching between separate applications.
GDV also connects genomic information with other NCBI resources, making it useful when investigating experimental datasets and published sequence information. NCBI provides detailed documentation, while its GitHub organisation hosts related bioinformatics projects.
This is free and open source software.
Key Features
- Provides access to annotated eukaryotic genome assemblies, including both NCBI RefSeq and selected independently annotated assemblies.
- Supports searching for organisms and selecting different genome assemblies through a graphical interface.
- Offers navigation by chromosome, scaffold, genomic coordinates, gene name and other recognised identifiers.
- Includes an ideogram view for selecting chromosome regions and understanding the location of genomic features.
- Provides an exon navigator for examining individual exons and moving between regions associated with a selected gene.
- Displays gene models, sequence variants, alignments and other molecular annotations using configurable data tracks.
- Integrates BLAST results, allowing sequence alignments to be examined in their genomic context.
- Supports uploading custom annotation data, including BED, GFF3, GTF, VCF, GVF and WIG files.
- Can stream remotely hosted alignment and annotation files, including indexed BAM, BigBed and BigWig datasets.
- Connects to external track hubs and supports custom collections of genomic tracks.
- Integrates data associated with NCBI resources including GEO, dbGaP and dbVar.
- Supports exporting sequence data and graphical views through the embedded Sequence Viewer.
- Provides shareable URLs that preserve selected display settings and track configurations for a limited period.
- Includes links to related NCBI tools for genome comparison, sequence downloads and further analysis.
Website: www.ncbi.nlm.nih.gov/gdv
Support:
Developer: National Center for Biotechnology Information
License: Public domain
Related Software
| Web-Based Desktop Genome Browsers | |
|---|---|
| Ensembl | Resource for geneticists, molecular biologists and other researchers |
| GDV | Exploration and analysis of eukaryotic RefSeq genome assemblies |
| HiGlass | Explore and compare genomic contact matrices and tracks |
| igv.js | Embeddable genomic visualization |
| NGB | Web-based NGS data viewer |
| JBrowse 2 | Modern React-based genome browser |
| trackplot | Visualize various next-generation sequencing data |
| Gosling.js | Builds interactive genomic visualisations from declarative specifications |
| D-Genies | Compares genome assemblies using interactive dot plots |
| IGV-Web App | Explores genomic alignments, sequence variants and gene annotations |
| Chromoscope | Explores structural variants and copy-number changes across genomes |
| CGView.js | Creates interactive circular and linear genome maps |
| Synflow | Visualises synteny and structural rearrangements across genomes |
| Genoverse | HTML5 scrollable genome browser |
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