Tag: Sequence Viewer

Change the way your graphs look with Genome Data Viewer’s enhanced settings

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).

Fig1
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).

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Check out improved tooltips in NCBI’s genome browsers and sequence displays!

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
Figure 1. Merged transcript and CDS pair tooltip.

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Join NCBI at PAG in San Diego, January 12–16, 2019

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.)

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November 28 NCBI Minute: Getting the Most from Track Hubs in NCBI’s Genome Data Viewer (GDV)

November 28 NCBI Minute: Getting the Most from Track Hubs in NCBI’s Genome Data Viewer (GDV)

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:

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November 14 Webinar: Variant Interpretation using NCBI Resources

November 14 Webinar: Variant Interpretation using NCBI Resources

Next Wednesday, November 14, 2018, NCBI staff will show you how to use NCBI’s genome browsers and other resources to interpret variants. The graphical displays of Genome Data Viewer (GDV) and Variation Viewer offer an interactive experience that allows you to explore NCBI’s rich collection of annotations, datasets and literature for deciphering your variant-associated data. In this presentation, we’ll step through case studies and show you how to quickly display relevant NCBI track sets — including the new RefSeq Functional Elements track, upload a file or remotely-hosted dataset and display these as a track, and use browser tracks to identify known variants, then assess variant functional and clinical significance and allele frequency. You will also learn how to navigate from the browsers to NCBI resources such as ClinVar, dbSNP and PubMed, for additional variant information.

Date and time: Wed, Nov 14, 2018 12:00 PM – 12:45 PM EDT

Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

 

 

See improvements in NCBI’s genome visualization and analysis tools at ASHG

GDV_homepage

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)

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Improved Search Now Available Across NCBI Databases

Earlier this year, we announced the release of a new and improved search feature that interprets plain language to give better results for common searches. This feature, originally developed in NCBI Labs and later released on the NCBI All Databases search, is now available across several NCBI resources: Nucleotide, Protein, Gene, Genome, and Assembly. Whether you are searching for a specific gene or for a whole genome, you will now retrieve NCBI’s best results regardless of the database  you search.

The image below shows the results for a search for human INS in the Nucleotide database. Even though this is a Nucleotide search, the results include relevant information from Gene, Protein, Taxonomy,  plus links to the NCBI reference sequences (RefSeq) as well as access to BLAST and the insulin gene region in NCBI’s genome browser, the Genome Data Viewer.KIS_nuccore_smallFigure 1.  The new natural language search result in the Nucleotide database from a search for human INS.

Try out this new search capability and let us know what you think. And keep visiting the NCBI Labs search page to try our latest experiments, which we’ll also announce here on NCBI Insights.

 

NCBI’s Genome Data Viewer now displays data from track hubs

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 “NCBI’s Genome Data Viewer now displays data from track hubs”

NCBI to retire Clone DB web interface

NCBI to retire Clone DB web interface

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.

The new BLAST widget seamlessly integrates your results into NCBI’s Genome Data Viewer (GDV)

The new BLAST widget seamlessly integrates your results into NCBI’s Genome Data Viewer (GDV)

Want to analyze your BLAST results in the context of a genome browser? Want to compare those results against other genome assembly annotations? The BLAST widget, a new browser feature, lets you do that. It provides direct access within GDV to execute and manage BLAST queries (blastn, tblastn) aligned to the specific assembly displayed in GDV.

To learn about this tool, keep reading or watch this short introduction video. Further details are in GDV’s help documents.

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