Introducing the NIH Comparative Genomics Resource (CGR)
NCBI is looking forward to seeing you in person at the International Plant and Animal Genome Conference (PAG XXIX), January 8-12, 2022 in San Diego, California. We’re especially excited to introduce our newest endeavor – the NLM initiative known as the NIH Comparative Genomics Resource (CGR)– a platform we are developing to support comparative analyses of sequenced eukaryotic research organisms. Understanding and supporting the needs of researchers is a fundamental element in the development of CGR and is critical to its future success in supporting a large and diverse collection.
Please join NCBI for the following events to learn more about CGR and how you can inform its development:
If you’ve ever tried searching for a genomic location in NCBI’s Genome Data Viewer (GDV) or Variation Viewer and found that your search term didn’t work, it’s time to try again! We recently expanded support for searches in our genome browsers using non-NCBI identifiers such as HGVS patterns (e.g. NM_001318787.2:c.2258G>A) and Ensembl IDs. You can also search by chromosome coordinates, cytogenetic band, assembly scaffold/component, disease/phenotype, dbSNP identifier, or RefSeq transcript/protein accession. We’ve gathered example searches in the table below.
When you search by single coordinate, SNP or dbVar ID, or HGVS, the browser view zooms to the location of the search result. A marker is automatically created to identify the searched position. For HGVS, the marker is labelled with the corresponding rsID, if there is one.
Figure 1. Variation Viewer showing results of search by an HGVS pattern, NP_001289617.1: p.Arg272Cys.
As always, please contact us if you have additional questions or suggestions about this or any other feature in GDV or Variation Viewer. You can use the Feedback button on the page or write to the NCBI Help Desk directly.
NCBI’s Genome Data Viewer (GDV) now supports visualization and analysis of nearly 400 submitter-annotated chromosome-level assemblies from the INSDC (GenBank/ENA/DDBJ). These submitter-annotated assemblies join more than 1,200 NCBI RefSeq-annotated assemblies available in GDV for hundreds of eukaryotes, spanning fungi, plants, fish, insects, and all major model organisms.
Figure 1. Submitter-annotated Malus domestica (apple) assembly displayed in GDV. GDV provides submitter-provided gene annotation, as well as some additional tracks including interspersed repeats identified by RepeatMasker and six-frame translations (not shown). Red boxes indicate useful tools and panels including a search box, an exon navigator, and interfaces to add user data and conduct NCBI BLAST searches.
The Genome Data Viewer (GDV) is now the comprehensive NCBI genome browser. The development of GDV led to a few different types of genome browsers along the way, each one originally delivering visual displays for particular datasets. We developed the 1000 Genomes Browser for variation data from the 1000 Genomes project, the dbGaP Data Browser for controlled-access sequence read alignment data, and the GeT-RM browser for Genome in a Bottle (GIAB) data.
The data displayed in these three browsers is now either obsolete and/or can largely be accessed from the GDV browser or other NCBI resources. Moreover, unlike GDV, these older browsers are no longer under active development and the data has not been updated to meet changing needs of the communities they were developed to serve. For these reasons we will retire these browsers in April 2022. Please see details below for more information on the data displayed in these browsers and how to access and display these data now through GDV and other means.
Did you know that you can see epigenomic or other experimental data in NCBI’s Genome Data Viewer (GDV)?
You can easily add aligned study results from GEO, SRA, and dbGaP as data tracks to GDV browser view. Just go to the Tracks button on the toolbar and select the menu option to Configure Tracks. Navigate to the ‘Find Tracks’ tab on the pop-up Configure panel (Figure 1).
Figure 1. Go to the ‘Tracks’ menu on the browser toolbar and select ‘Configure Tracks’ option. This will launch a panel where you can add, configure, remove, and search for data tracks. Go to the ‘Find Tracks’ tab to search for tracks to add to your browser view. Note: spaces act as AND operators in the search, and wildcards are accepted.
The Bulk Sequence-Cytogenetic Conversion Service tool at NCBI will be retired in April 2022. This tool obtained cytogenetic locations for a list of annotated genes, SNPs, or assembly coordinates from human, fruit fly, mouse, or rat genomes. It also obtained sequence coordinates for cytogenetic locations for these genomes. This web service will be retired due to low usage and obsolescence.
The underlying cgi (bp2band) will be retained and continues to drive the Ideogram service within the Genome Data Viewer (GDV) and the Genome Decoration Page. Researchers interested in understanding where features are located relative to chromosome cytogenetic banding should check out the Genome Decoration Page, where you can enter a file of genome annotations and display them on a ideogram of your assembly of interest. You can also go directly to a cytogenetic location on a genome using the search box in the GDV genome browser.
Do you need to know which of the many NCBI dbSNP variants annotated near your region of interest are likely to be functionally or clinically significant? Figure it out with the track labelled ‘ClinVar variants with precise endpoints’, available on sequence display viewers at NCBI, including the Genome Data Viewer (GDV) and Variation Viewer!
This track shows variation annotation, including single nucleotide variants and other short variants (e.g. insertions, deletions, etc.) in the NCBI ClinVar database and provides pathogenicity and other metadata. The ClinVar track is displayed next to the default NCBI and Ensembl gene annotation tracks and other NCBI-provided dbSNP and RNA-seq expression tracks.
Figure 1. GDV showing ‘ClinVar variants with precise endpoints’ track next to NCBI human gene annotation. Tracks are color coded for quick and easy interpretation. Legend is also provided.
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Introducing GaPTools for dbGaP Submitters
This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools uses the same preliminary validation checks as the dbGaP submission portal.
