Have you ever wanted a list of the genes you’re looking at in the browser – maybe to give you a starting point for candidate gene analysis, or to cross-reference with other data?
In response to your feedback and helpful discussions with you, we’re excited to announce a new option to download gene annotation data directly from the web sequence viewers and browsers.
This new feature lets you get a table of gene names, coordinates and other helpful information from your genomic region of interest.
Go to the Download menu on the toolbar of the graphical viewer to find options for getting sequence and annotation data.
You can download information from any gene annotation tracks in view. You can choose from three tabular formats: GFF3, CSV (comma-separated value), and BED (Browser Extensible Data).
The CSV option gives you a “human-readable” table with the gene symbol, name, coordinates, strand, and NCBI Gene ID (if applicable). You can open this table directly in MS Excel or your spreadsheet program of choice.
The BED option gives you a 6-column BED table for the gene feature. You can manipulate BED and GFF3 files on the command line (e.g. using bedtools) or load them into other graphical tools that support these file types.
You have the option to include or exclude transcript, CDS, and exon annotation from the GFF3 format. Currently, only gene features are reported for the BED and CSV formats.
If you’d like to know more about downloading sequence and track data from the NCBI graphical sequence viewer, go here.
We hope you’ll enjoy exploring this new feature. Please contact us if you’d like to provide further feedback on downloads or anything else regarding the NCBI genome browser and graphical sequence viewers.