Tag: Genome Data Viewer (GDV)

Announcing the RefSeq annotation of rat mRatBN7.2!

Announcing the RefSeq annotation of rat mRatBN7.2!

NCBI RefSeq has finished its initial annotation of the new rat reference assembly, mRatBN7.2, recently released by the Darwin Tree of Life Project at the Wellcome Sanger Institute. This is the first coordinate-changing update to the rat reference since the 2014 release of Rnor_6.0 from the Rat Genome Sequencing Consortium and brings the rat assembly into the modern age with a nearly 300x increase in contig N50 and 9x increase in scaffold N50 lengths. It’s a major improvement!

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View intron feature evidence in the Genome Data Viewer and Sequence Viewer

Are you a researcher who works on gene biology and are interested in alternative splice patterns in your gene or genes of interest?  If so, be sure to explore the intron feature evidence available in graphics views of genome assemblies annotated by NCBI. You can view the NCBI evidence used for calling splice variant for genes, add other intron feature evidence tracks, and use new display and filter options that make it easier to interpret the data .

Figure 1. Graphical view of the monoamine oxidase gene (MAOA, MOAB) region on the human X  chromosome showing intron features tracks (‘RNA-seq intron features, aggregate’ and ‘Intropolis RNA-Seq intron features’). Mousing-over an intron feature activates a tooltip that shows details such as the number of reads with the splice site, the location on the chromosome, the length of the intron and the donor and acceptor bases at the splice site. The Intropolis track was added through the search feature of the Configure Tracks menu and configured (bottom menu) so that the features were sorted by strand and filtered so that only features with greater than 500 reads appear.

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Improved chromosome searching in Genome Browsers

Are you interested in searching for a chromosomal region in a genome, but don’t know how to write the correct query?  The good news is that the NCBI Genome Data Viewer (GDV) now supports a much wider array of search options. Some examples are listed below:

  • chr1:1,500,000-2,000,000
  • chr2: 1.5M – 2M
  • chr2: 1.5M-2,540.2K
  • 2:1,500,000-2,000,000
  • 3: 21.33M – 22.01M
  • 3: 21.335M..21.337M
  • chr1:1,500,000 / 200
  • chr1:101,500,200
  • 1:101,500,200
  • 1:1,500K/0.5K
  • chr5
  • 10

You can use any of these queries or the ones described below for assembly aliases either on the GDV landing page or in the GDV search box (Figure 1).

Figure 1. The search boxes on the GDV landing page (left) and within the GDV graphical interface (right) showing queries with chromosome aliases for the domestic cat. Continue reading “Improved chromosome searching in Genome Browsers”

Coronavirus host gene regulatory elements now annotated by RefSeq Functional Elements

The COVID-19 pandemic has drawn attention to the human host genes associated with SARS-CoV-2 entry and to the elements that regulate expression of these genes. At NCBI, we have prioritized curation of experimentally validated regulatory elements for these genes in the RefSeq Functional Elements project. Our annotations include several enhancers, promoters, cis-regulatory elements and protein binding sites, among other feature types.  We have annotated 236 regulatory features for 27 distinct biological regions in the latest human Annotation Release (109.20200522) including regulatory elements for the ABOACE2, ANPEPCD209CLEC4GCLEC4MCTSL, DPP4,and TMPRSS2 genes

You can view our regulatory element to target gene linkages in the regulatory interactions track using our new track hub that we recently announced.  You can also see the biological regions and features tracks. These have functional and descriptive metadata, including biological region summaries, experimental evidence types, publication support and more.

The example in Figure 1 shows RefSeq Functional Element feature annotation in NCBI’s Genome Data Viewer (GDV) for the ABO gene region (GRCh38, NW_009646201.1: 73,864-103,789) the determiner of the human ABO blood group. A genome-wide association study recently identified non-coding  ABO variants associated with COVID-19 disease severity (PMID:32558485), which map to some of the RefSeq Functional Elements in this region.ABO region showing biological regions in GDVFigure 1. The human ABO gene region in the NCBI GDV displaying the RefSeq Functional Element features.  The biological regions aggregate track shows underlying feature annotation for an ABO upstream enhancer (LOC112637023),  promoter region (LOC112679202),  +5.8 intron 1 enhancer (LOC112679198),  a 3′ regulatory region (LOC112639999), and a +36.0 downstream enhancer (LOC112637025).  Functional Element features include numerous enhancers, promoters, cis-regulatory elements and protein / transcription factor binding sites.

We have more information about RefSeq Functional Elements on our website, including data download and extraction options. Stay tuned to NCBI Insights and other NCBI social media for future announcements about RefSeq Functional Elements!

Non-human variation data from EVA now available in the Genome Data Viewer

You can now view SNP variation data for many commonly studied animals and plants – including mouse, cow, Drosophila, Arabidopsis, maize, cabbage, and many more – in the Genome Data Viewer (GDV) and other graphical sequence viewers. This data is streamed from the European Variation Archive (EVA)  at the European Bioinformatics Institute (EBI).

On any NCBI graphical sequence view you can use the Configure Tracks menu and the Track Configuration Panel to add the track for the EVA RefSNP data. This track is available through the left-hand tab for Remote Variation Data (Figure 1).  The EVA RefSNP track displayed on the pig (Sus scrofa) chromosome 12 graphical view is shown in Figure 2.

Config_tracksFigure 1. The Track Configuration panel showing the Remote Variation Data tab and he EVA RefSNP Release 1 track. Select the track checkbox and click Configure to load the track.

pig_snpsFigure 2. The graphical sequence viewer showing the region of the growth hormone gene on pig chromosome 12 (NC_010454.4) with the EVA RefSNP Release 1 track at the bottom.  The track header has an (R) and a green highlight to indicate that it is remote data streamed from an external website. NCBI is not responsible for the content or availability of these data. 

The EVA SNP FTP site has more information about the EVA SNP data release.

Please contact us using the Feedback link on the graphical view to let us know what you think and how we can further improve your experience with the NCBI genome browsers and graphical sequence viewers

 

dbVar clinical and common structural variants track hub now available

dbVar, NCBI’s database of large-scale genetic variants, has a new track hub for viewing and downloading structural variation (SV) data in popular genome browsers. Initial tracks include Clinical and Common SV datasets. dbVar’s new track hub can be viewed using NCBI’s Genome Data Viewer through the “User Data and Track Hubs” feature (Figure 1) and other genome browsers by selecting “dbVar Hub” from the list of public tracks or by specifying the following URL.

https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt

Main_Track_Hub_Dial

Figure 1. Loading the dbVar track hub in the Genome Data Viewer. The Track Hubs feature on the left-hand column of the browser allow you to add the track by searching for it or by entering the direct URL. You can select the specific tracks —  for example, “NCBI curated common SVs: All populations” — to load from the Configure Track Hubs dialog. Continue reading “dbVar clinical and common structural variants track hub now available”

NCBI staff to present 3 posters at Advances in Genome Biology and Technology (AGBT), February 2020

Next week, NCBI staff will attend AGBT in Marco Island, Florida. On Tuesday, February 25, 2020, three posters from NCBI staff will be on display from 4:40 p.m. – 6:10 p.m. during the Poster Session and Wine Reception in the Banyan and Calusa Ballroom Foyers, Levels 1 and 3. Read on to learn a little bit about what we’ll be presenting.

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Try out our new table download options from the NCBI genome browsers and sequence viewers!

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.

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NCBI on YouTube: Get the most out of NCBI resources with these videos

Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.

Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips

This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.

Continue reading “NCBI on YouTube: Get the most out of NCBI resources with these videos”

Bulk track hub settings now in Genome Data Viewer

You now have access to bulk settings options for track hubs  in the Genome Data Viewer (GDV) and Sequence Viewer. These settings allow you to pick the default tracks that load into the viewer from your chosen track hub.  You can access the bulk options menu for by clicking on the collapsed menu  or “hamburger” icon (stack of horizontal bars) at the right end of the track grouping in the Configure Track Hubs dialog (Figure 1).Bulk_SettingsFigure 1. The Configure Track Hubs dialog in GDV. You can activate the bulk settings menu for a connected track hub by clicking on hamburger icon at the right of the track grouping.  Clicking Select Default tracks checks on all of the tracks in that grouping, Smoothed PhyloCSF in this case.  Continue reading “Bulk track hub settings now in Genome Data Viewer”