Learn about the NIH Comparative Genomics Resource (CGR) Project
The Biodiversity Genomics conference will take place virtually, October 2-7, 2022. This event is hosted by the Earth BioGenome Project and is open and free for all to attend.
NCBI staff will present a variety of recorded talks and posters highlighting various elements of the NIH Comparative Genomics Resource (CGR), including NCBI Datasets and the Comparative Genome Viewer (CGV). CGR is a multi-year National Library of Medicine (NLM) project to maximize the impact of eukaryotic research organisms and their genomic data resources to biomedical research. NCBI is charged with leading CGR development and engaging genomics communities. The CGR project will facilitate reliable comparative genomics analyses for all eukaryotic organisms in collaboration with the genomics community.
The NCBI Datasets SARS-CoV-2 taxonomy page brings you both SARS-CoV-2 genomes and proteins, basic information about SARS-CoV-2, and connections to related NCBI pages, all in one place (see Figures 1 and 2).
Figure 1. NCBI Datasets SARS-CoV-2 taxonomy page. For command-line access, try the datasets command-line tool (top box). For customized filtering options, check out NCBI Virus (bottom box).
If you scroll down the taxonomy page you will find a table of SARS-CoV-2 proteins, each with “Actions” that provide the option to download a package of protein sequences from all annotated SARS-CoV-2 genomes (Figure 2), as well as links to NCBI Gene and the protein sequence from the reference genome.
Figure 2. NCBI Datasets SARS-CoV-2 taxonomy page (cont’d).Click the blue download button to download a package of all SARS-CoV-2 genomes (6 M and counting as of 7/15/22), or just the SARS-CoV-2 reference genome (top box). Below that you see a table of SARS-CoV-2 proteins, each with “Actions” available through the three-dot menu that provides the option to download a package of protein sequences from all annotated SARS-CoV-2 genomes (bottom boxes).
We want to hear from you! Check out the new SARS-CoV-2 taxonomy page and let us know what you think. Contact us with questions or feedback.
We are excited to introduce new and useful updates to the Datasets genome table that let you quickly find and download a genome dataset including genome, transcript and protein sequence, annotation, and a data report.
The new genome table includes many new features and benefits (see Figure 1). With the new genome table you can:
GCC2022 brings together hundreds of researchers, trainers, tool developers, software engineers, and computational infrastructure providers, all addressing common challenges in data intensive science using the Galaxy data integration and analysis platform. This will be an in-person meeting with limited support for remote attendees.
Check out NCBI’s schedule of activities:
NCBI Datasets, a new resource for accessing NCBI genome data in Galaxy
As part of an ongoing effort to modernize and improve your experience, NLM’s NCBI Datasets is introducing all-new genome pages. These pages make it easier for you to browse and download genome sequence and metadata, and navigate to tools such as the Genome Data Viewer (GDV) and BLAST.
To get started, search NCBI Datasets by assembly accession (e.g., GCF_016699485.2), assembly name (e.g., bGalGal1.mat.broiler.GRCg7b), WGS accession (e.g., JAENSK01), or species name + genome (e.g., chicken genome), and click on the title in the box. See the top red arrow in Figure 1 below where we search for ‘chicken genome’.
Figure 1: Finding the chicken reference assembly. A search for ‘chicken genome’ returns a box that provides a quick link to the new genome page (middle red arrow). From there, the download button (bottom red arrow) allows you to select the files you need (see ‘Download Package’ window on the left) along with a detailed metadata report that includes all the metadata on the web page. Continue reading “Introducing NLM’s new NCBI Datasets genome page!”→