Primer-BLAST now has a “Primers common for a group of sequences” submission tab that allows you to design primers for a group of highly similar sequences. For example, you may want test for expression of any transcript of gene rather than a specific splice variant, so you want to design primers to cover all transcript variants. Or you may want to design primers that will amplify the same gene in closely related bacteria strains. To find primers for a group of related sequences, Primer-BLAST aligns the longest sequence to the rest to find common regions. It uses these to limit the locations of primers. The longest sequence is also used as the representative template sequence in the results. Figure 1 shows an example search for primers that will amplify all of the 15 splice variants for the human TP53 gene.
Figure 1. Primer-BLAST submission page and results for primers designed for the human TP53 transcripts. Top panel: The submission form with the “Primers common for a group of sequences” selected and the 15 RefSeq transcript accessions for TP53. Middle panel: The graphical results showing the longest sequence (NM_001126114.3) as the representative template, the locations of the primer pairs, and the alignment of the other template sequences. Bottom panel: An individual primer pair showing the locations on each of the template sequences.
Please try out this new feature and let us know what you think!
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:
chr2: 1.5M – 2M
3: 21.33M – 22.01M
chr1:1,500,000 / 200
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).
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 ABO, ACE2, ANPEP, CD209, CLEC4G, CLEC4M, CTSL, DPP4,and TMPRSS2genes.
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.Figure 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!
Version 3.4.1 of Genome Workbench, NCBI’s sequence annotation and analysis platform, includes new features for the Multiple Sequence Alignment View, the Graphical Sequence View and the Sequence Editing and Submission Package as well as a number of other improvements and bug fixes.
In the Multiple Sequence Alignment View, you can now export publication quality graphics (Save As PDF/SVG … , Figure 1). In the Graphical Sequence View you can now search by locus tag, use improved search capabilities for genes by locus and can better display the selected location in the feature editing dialog when annotating a sequence.
Figure 1. A multiple alignment view in Genome Workbench highlighting the new ability to save presentation quality image files (Save As PDF and SVG formats).
In the Sequence Editing and Submission Package, we rearranged the controls in the Table Reader dialog to fit onto smaller screens and improved importing feature tables that contain mat-peptides (mature peptide) features.
Bug Fixes and Improvements
We have made a number of other fixes and improvements. For MacOS users we fixed blurry text in some dialogs, fixed the copy to clipboard problem, and improved support for the latest Catalina version. We also fixed a crashing problem in the Active Object Inspector interface. You should also see improvements in loading SNP data and better recovery in cases of power outages or other events causing local file corruption.
In the Sequence Editing and Submission Package, we fixed a bug that occurred when applying miscellaneous descriptors and structured comment fields using the Table Reader and an issue with using a PubMed ID to look up a publication.
Please see the extensive help documentation including FAQs, videos, and tutorials linked to the Genome Workbench homepage for more information and examples on how to use Genome Workbench in your research.
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.
Figure 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.
Figure 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.
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, 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.
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.
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.
NCBI’s genome browsers and graphical sequence viewers now allow you to view BAM alignments sorted by haplotype tag. This option is useful for analyzing variants within a sequenced sample and can help you detect or validate structural variants.Figure 1. Remote BAM alignment data sorted by haplotype tag in the Genome Data Viewer. The remote BAM file was added through the “User Data and Track Hubs” feature in GDV. You can load the remote BAM for this example through https://go.usa.gov/xpM9c. The sorted display shows that haplotype 1 contains a significant deletion in this region relative to haplotype 2 and the reference genome assembly. Aligned reads not assigned a haplotype tag in the BAM file are grouped under the heading “haplotype not set” (not shown).