On June 18, 2019, NCBI’s Sanjida Rangwala will demonstrate the rich data visualization capabilities of NCBI’s genome browser at a conference that is part of the Rocky Mountain Genomics Hackcon. As mentioned in a previous post, NCBI staff will also participate in an NCBI-style Hackathon as part of the larger event. The genome browser presentation and demonstration will show you how to create visuals that provide insights and show connections among genes, transcripts, variation, epigenomics and GWAS data from NCBI sources. You will also see how you can upload your own data and embed NCBI viewers on your own pages.
Next week, NCBI staff will attend the Plant and Animal Genome (PAG) Conference. We have several activities planned, including 1 booth (#223), 4 workshops, 1 talk and 2 posters.
Read on to learn more about what you can look forward to if you’re attending PAG this year. (Note: The listed times are Pacific time.)
In 2016, NCBI introduced the Genome Data Viewer (GDV). This past May, the GDV replaced the aging Map Viewer. Over the past year, NCBI has kept you updated about GDV through announcements, webinars, and blogs. Now you can gather information and get an overview of all the changes to GDV in person at ASHG!
Check out Poster 1670F “What’s new with NCBI tools for genome visualization and analysis.” on Friday, Oct. 19 from 3 PM to 4 PM
(Exhibit Hall, Ground Level)
This year, we have two CoLabs – interactive sessions where you can learn about freely available NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG in two weeks!
The Genome Data Viewer’s (GDV) browser display now supports content provided in track hubs. This new GDV feature, summarized in this short video, extends the genome browser’s capability when it comes to viewing user-supplied data tracks alongside NCBI-provided tracks. You now have multiple options to analyze your data that include uploading your data (file/URL), streaming individual files from a remote location and/or connecting to a track hub. In all instances, GDV recognizes a variety of popular file formats with support for additional file formats planned. In the display, you can now also easily distinguish user-supplied tracks by their green-tinted track labels. Continue reading
Starting in April 2019, the sequence content of Clone DB will be frozen, and its web interfaces will no longer be available. NCBI will continue to produce and make genomic clone placements available as annotations in NCBI’s Genome Data Viewer (GDV) using the sequence data currently in Clone DB. These placements and their corresponding underlying (now static) library and sequence data will also be accessible on the Clone DB FTP site.
The collection of Clone DB records for cell-based (integrated) gene targeting and gene trap libraries will also be retired in January. These data were provided to Clone DB by MGI. Clone DB users should refer to MGI for their continuing research needs.
Please contact us with any comments, concerns, or if you need help with the use of Clone DB data.
Clone DB was originally implemented as the Clone Registry during the human and mouse genome projects. In subsequent years, it expanded to represent clone-associated data for a broad range of organisms. Clone DB has been a valuable resource connecting users with information and reagents for genomic and cell-based clones. However, with the advent of short read sequencing, fewer and fewer genomic clone end and insert sequences are submitted to NCBI every year, and the usage of and need for Clone DB has dropped significantly.
Several of the latest videos on the NCBI YouTube channel highlight NCBI resources. Subscribe to the channel to see all our new videos.
A brief introduction into how the BLAST widget, a new addition to the Genome Data Viewer, helps you see your BLAST results in the context of assembled genome sequences.
Highlights in release 109:
- A total of 20,203 protein-coding genes and 17,871 non-coding genes were annotated.
- The number of annotated curated transcripts increased by 17% and genes with two or more curated alternative variants increased by 8%.
- The annotation includes 6,862 features and 2,075 GeneIDs for non-genic functional elements, such as regulatory regions and known structural elements. For example, see the opsin locus control region (OPSIN-LCR).
On October 24, 2017, we announced the replacement of NCBI’s Map Viewer with the Genome Data Viewer (GDV) . As described in that announcement, the Map Viewer web interface will be removed in one week on May 2, 2018. Map Viewer links will be redirected to the GDV home page. Map Viewer static data will remain on the NCBI FTP site. Please review details related to the FTP content in our February announcement.
Please contact us with any comments and concerns, or if you need more help with the transition from Map Viewer to GDV.
In October of last year, we announced the replacement of NCBI’s Map viewer with the Genome Data Viewer (GDV). Here are some additional details on how to access to the older Map Viewer FTP content going forward and some information to help you with the transition to GDV.
As we announced last fall, we are no longer updating the data content of Map Viewer FTP directories. To help avoid any confusion over the meaning of the directory names, we will alter the CURRENT and PREVIOUS directories under the species directories in the Map Viewer FTP area so that they no longer point to data. However, the existing data will still be available on the FTP site.