Author: NCBI Staff

NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data

Millions of SARS-CoV-2 samples from around the world have been made publicly available as assembled and unassembled sequence data in GenBank and the Sequence Read Archive (SRA). Now you can find sequences with a particular mutation by searching with the protein and the amino acid change (e.g. S:F486V). Visit our SARS-CoV-2 Variant Overview on NCBI Virus and click on the ‘Mutation’ tab to get started (Figure 1).

Figure 1: SARS-CoV-2 Variants Overview. Arrows indicate important features on the page, including the “Lineages” and “Mutations” tabs to switch between views, the search box, and the information box describing the mutation format. The results are also indicated, including a summary of the total records found that contain the searched term as well as the results table. Continue reading “NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data” →

NCBI SARS-CoV-2 Resources Page Will Redirect Soon

End of the COVID-19 Public Health Emergency

During the COVID-19 pandemic, we provided the NCBI SARS-CoV-2 Resources Page as a central location to help you quickly and easily find our SARS-CoV-2 related content and tools. Since the federal public health emergency is now over, this page will be redirected to the SARS-CoV-2 Data Hub in NCBI Virus effective August 1, 2023.

Don’t worry! All this information will remain available. Check out the NLM Knowledge Base to access a list of NCBI SARS-CoV-2 data and tools.

Stay up to date

Questions?

If you have questions or would like to provide feedback, please reach out to us at info@ncbi.nlm.nih.gov.

Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI

Have you ever wondered how your genetic make-up is different from your neighbor’s? The National Human Genome Research Institute (NHGRI)-funded Human Pangenome Research Consortium (HPRC) has built an initial version of a pangenome reference – a collection of new human reference genome sequences representing 47 individuals from across the globe. Pangenome graphs relate the sequences from the different genomes to one another. The pangenome allows researchers to compare these DNA sequences and get a more detailed view of the range of human genetic variation. This is the first step toward the HPRC’s goal of building a pangenome reference comprised of the genomes of 350 individuals from diverse genetic backgrounds. Continue reading “Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI” →

Making Discoveries in Canine & Human Oncology using the NIH Comparative Genomics Resource (CGR)

Do you use model organisms to study specific genes or genetic variations to research a particular human disease or phenotype? The National Institutes of Health (NIH) Comparative Genomics Resource (CGR) offers a cutting-edge NCBI toolkit of high-quality genomics data and tools to help you with comparative genomics analysis for eukaryotic organisms.

As comparative genomics advances, an increasing number of model organisms (established and emerging) are relied upon for studying human health. Dog genomes have been extensively studied and characterized and many genetic variations have been identified that are associated with canine hereditary diseases. Among these are several cancers which are common in both species, making dogs an ideal model for human disease progression and treatment. Continue reading “Making Discoveries in Canine & Human Oncology using the NIH Comparative Genomics Resource (CGR)” →

New! May 2023 Release of Stand-Alone PGAP

We are happy to announce the release of a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP) with many exciting new features.

Improved user interface

This version has an improved user interface that takes the genome FASTA file and associated organism name directly on the command line. For example, to annotate a Vibrio cholerae genome sequence in the file Vchol.fasta:

pgap.py -r -g Vchol.fasta -s 'Vibrio cholerae' -o Vchol.annot

For more details visit our Quick Start page. Continue reading “New! May 2023 Release of Stand-Alone PGAP” →

New! The Comparative Genome Viewer (CGV) Dot Plot

Get a High-Level View of Assembly-Assembly Alignments

New feature! We added an alternate view in the Comparative Genome Viewer (CGV) that shows a dot plot (also known as a 2D plot) comparing two related genome assemblies. This added view provides a high-level overview of the assembly-assembly alignment. Dot plots help you find large genome rearrangements such as translocations or segmental duplications more easily.

Using the Dot Plot View

From the main CGV view, you can access the dot plot by clicking on the new ‘Go to dot plot view’ link.
Click on a cell in the plot to zoom to a pairwise comparison between two chromosomes.
You can return to the main CGV view by clicking on ’Go to ideogram view’.
When you return to the ideogram view from the chromosome level dot plot view, you’ll see the same chromosomes you were looking at in the dot plot. Here, you can zoom further to investigate gene annotation and obtain alignment details.

Continue reading “New! The Comparative Genome Viewer (CGV) Dot Plot” →

Important Update! Changes to ASSEMBLY_REPORTS and GENOME_REPORTS on FTP

Do you currently access genome assembly data through the FTP site? We are consolidating information provided in the ASSEMBLY_REPORTS and GENOME_REPORTS directories on the genomes FTP site to simplify access and ensure that you have the most accurate, up to date, and consistently reported data.

The assembly_summary files in the ASSEMBLY_REPORTS directory are gaining information in newly added columns 24-38, including statistics about the assembly (size, GC content, genome size, and number of sequences) as well as details about the provided annotation (number of genes, annotation name and date). See example below (Table 1). Check out the README for more details about the contents of the summary files. Continue reading “Important Update! Changes to ASSEMBLY_REPORTS and GENOME_REPORTS on FTP” →

A Modernized ClinicalTrials.gov Website is Coming

In June 2023, the modernized version of ClinicalTrials.gov will become the primary site. This is a multi-year effort to modernize ClinicalTrials.gov to deliver an improved user experience on an updated platform that will accommodate future growth and enhance efficiency. In response to your feedback, the updated website includes a modern look and feel as well as improved functionality for searching, viewing, and downloading information about clinical studies.

Changes Across the Website

The new ClinicalTrials.gov website has a streamlined design with a color scheme and layout that is visually appealing, easy to read, and based on the U.S. Web Design System – consistent with other federal government websites. We’ve improved navigation with simple web components, such as left-side menus and expandable accordions, so you can quickly locate information. We’ve also added more plain language guidance and educational content. In addition, ClinicalTrials.gov has been optimized for mobile devices, so you can access this resource anytime from anywhere. Continue reading “A Modernized ClinicalTrials.gov Website is Coming” →

Download Assembled Genome Data Programmatically with NCBI Datasets

As previously announced, NCBI’s Assembly and Genome record pages will be redirected to new NCBI Datasets pages in June 2023. The NCBI Datasets Command Line Interface (CLI) tools provide easy, straightforward programmatic downloads of assembled genome sequence data. We invite you to check them out and let us know what you think!

Features & Benefits of NCBI Datasets

Get assembled genome sequence, annotation, and metadata, including transcripts and proteins, in one easy step.
Querying is easy and flexible! Retrieve data using organism name, assembly accession, or BioProject accession.
Request data for multiple assemblies in one request – it is now simpler and faster to download large amounts of data.
Metadata is derived from multiple databases and metadata schemas are documented.

Continue reading “Download Assembled Genome Data Programmatically with NCBI Datasets” →

Revolutionize your research with the NIH Comparative Genomics Resource (CGR)

Unlock the full potential of eukaryotic research organisms and their genomic data with the National Institutes of Health (NIH) Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses through community collaboration as well as an NCBI toolkit of interconnected, interoperable data and tools.  

Comparative genomics is a field of study that uses the genomes of many different organisms to help us understand basic biological processes and human disease. NCBI is developing CGR to help researchers take full advantage of the rapidly growing number of eukaryotic organisms that, due to recent technological advances, now have sequenced genomes and associated data that can be used in these types of studies. Its NCBI toolkit offers new and modern resources for such analyses, and its emphasis on community collaboration brings new opportunities to share and connect data. Continue reading “Revolutionize your research with the NIH Comparative Genomics Resource (CGR)” →