Earlier this year, NCBI announced plans to retire the Clone DB web interface. Pursuant to this retirement, starting on May 27, 2019, all web pages associated with Clone DB and CloneFinder will redirect to this blog post. Links to Clone DB from the NCBI home page will also be going away.
Did you know you can easily switch between gene feature modes in NCBI’s graphical sequence displays like Sequence Viewer and GDV? You may need to configure gene tracks to suit your needs if, for example, you need to conduct analyses or present quality images.
Use one of two easy access points to the gene configuration menu to show the gene bar, the single line gene model or the expanded modes that show transcripts and CDSs.
If you need to change your graph type – say, from histogram to line graph or a heat map – in Genome Data Viewer (GDV), you can now do so with a few clicks.
Click on the track name of any graph track to change the display (see Figure 1A, B and C).
Figure 1. Click on a track name to expose the graph settings menu (A). Set graph display style (B) to histogram, heat map or line graph (C).
We’ve recently improved the tooltips for gene features in NCBI’s graphical sequence displays in Genome Data Viewer (GDV) and on many resource pages, such as Gene and dbSNP. These enhancements include quick details and helpful links about the feature and gene.
Figure 1. Merged transcript and CDS pair tooltip.
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.)
This webinar is intended for both new and experienced Track Hubs users.
Join us November 28, 2018 at noon EST for an NCBI Minute explaining what GDV’s Track Hubs are and how they can help you in your research.
Register here: https://bit.ly/2PUHBqz
After this webinar, you’ll be able to:
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)
As you know, NCBI will be attending American Society of Human Genetics (ASHG) 2018 in San Diego.
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.
