Tag: Comparative Genomics Resource (CGR)

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

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)” →

Updated Design! NCBI Datasets Homepage

Updated Design! NCBI Datasets Homepage

The updated NCBI Datasets homepage has a fresh new look and feel, making it easier for you to use. Now more prominent at the top of the page, you can enter and select the scientific or common name of the species you’re interested in and go directly to the NCBI Datasets Taxonomy page for that species. 

We added a “How to use NCBI Datasets” section, providing you an overview of what’s available in NCBI Datasets. You can see example species with links to NCBI Datasets pages relevant to that species. For example, for Ursos arctos (brown bear), we include links to the Taxonomy page, the genome table showing all available genomes, the reference genome page for UrsArc1.0, as well as connections to BLAST and the Ursos arctos gene table. 

You can still use the tab bar at the top of the homepage to easily navigate to our genome and gene tables or check out our documentation.  Continue reading “Updated Design! NCBI Datasets Homepage” →

Navigating Between BLAST and iCn3D

Navigating Between BLAST and iCn3D

Explore protein structures and sequences quickly and easily 

Have you ever come across an unfamiliar protein in your BLAST results? With the newly added ‘AlphaFold Structure’ link (Figure 1), you can now explore its structure as predicted by AlphaFold in iCn3D. The iCn3D Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool with interactive displays of 3D structure, 2D topology, 1D sequence and annotation.  

Features & Benefits
  • Upload AlphaFold structures to iCn3D directly 
  • Use the structure search feature to find structures of interest 
  • Understand important features of the structures, such as disease-associated variations (ClinVar), genetic variations (dbSNP), or chemical modifications (PTM) 
  • Identify similarities and differences between AlphaFold predictions and experimentally determined structure 
  • Gain insights into the structural characteristics and properties of the molecules 
  • Use iCn3D in different platforms (Jupyter Notebook, Virtual Reality, and Augmented Reality) 
  • Easily integrate iCn3D using scripted workflows (node.js, python) to analyze large sets of structures 

Continue reading “Navigating Between BLAST and iCn3D” →

Now Available! Faster BLAST Searches with New Nucleotide Databases

Now Available! Faster BLAST Searches with New Nucleotide Databases

NEW in BLAST! We made smaller nucleotide databases to help you find the sequences you need faster and easier. You can now find these databases on the main nucleotide BLAST search page (Figure 1) and even download them (Databases: nt_euk, nt_prok, nt_viruses, nt_others). They are separated by organism type, such as eukaryotes, prokaryotes, viruses, and others (including synthetic sequences).

Figure 1. The database selection section of the main nucleotide BLAST page with the ‘Experimental databases’ radio button selected. You can choose one or more of the organism database subsets for your search.  Continue reading “Now Available! Faster BLAST Searches with New Nucleotide Databases” →

RefSeq Release 218

RefSeq Release 218

RefSeq release 218 is now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

As of May 1, 2023, this full release incorporates genomic, transcript, and protein data containing:

Flip Chromosomes in the Comparative Genome Viewer (CGV) to Analyze Syntenic Regions More Easily

Flip Chromosomes in the Comparative Genome Viewer (CGV) to Analyze Syntenic Regions More Easily

We are excited to introduce a new user-validated feature in the Comparative Genome Viewer (CGV) making it easier for you to analyze inverted regions. You can flip the orientation of one of the aligned chromosomes in the view, so the sequence and gene order is facing the same direction for both assemblies.  

What’s new?

When looking at genome alignments in CGV, you may find related sequence regions that are inverted in one assembly relative to another. It may be difficult to tell if gene synteny (order and orientation) is conserved in these inverted segments because the relative gene order is reversed.  

Now available! Look for the “flip” button on the left side of either the top or bottom chromosome (Figure 1).   

  • Clicking on the “flip” button will reverse the direction of the chromosome.  
  • Reverse-orientation alignments will still show up as purple but will have an “un-twisted” style.  

Continue reading “Flip Chromosomes in the Comparative Genome Viewer (CGV) to Analyze Syntenic Regions More Easily” →

New annotations in RefSeq!

New annotations in RefSeq!

In February and March, the NCBI Eukaryotic Genome Annotation Pipeline released forty-two new annotations in RefSeq for the organisms listed below. Additionally, interim builds for over sixty species were run during that time period to fix some issues with gene symbol assignment.

New Improvements! Try out our Foreign Contamination Screen (FCS) Tool

New Improvements! Try out our Foreign Contamination Screen (FCS) Tool

Want to submit high-quality data quickly and easily to GenBank? Check out our Foreign Contamination Screen (FCS) tool, a quality assurance process that you can run yourself. FCS offers enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to GenBank. We recently made several improvements to make the tool even easier to use! 

What’s New?
  • Now quicker and easier to run!  
  • Decontaminate your genome with just one extra step. 
    • Save the removed sequences in a separate file, if desired.  
  • More accurate!  
  • Find more contaminants with improved coverage of prokaryotes, protists, and more. 
  • Screen your genome on the cloud in minutes. 

Continue reading “New Improvements! Try out our Foreign Contamination Screen (FCS) Tool” →

New Way to View and Download Related Genes

New Way to View and Download Related Genes

Effective June 2023, the HomoloGene records will redirect to the Datasets Gene Table

Do you use HomoloGene to view and download data? You can now access updated homology data from NCBI Datasets through the Datasets Gene Table with connections to NCBI Orthologs. Go directly from a HomoloGene record to the Datasets Gene Table that will give you access to up-to-date sequence data and metadata. NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

The Datasets Gene Table provides connections to the NCBI Ortholog interface (Figure 1) that provides the following data: 

  • Orthology data based on an updated algorithm that identifies orthologs spanning > 500 vertebrate species 
  • Similar gene data based on protein architectures that spans all eukaryotes 

Continue reading “New Way to View and Download Related Genes” →

Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue

Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue

The 2023 Nucleic Acids Research Database Issue features papers from NCBI staff on GenBank, Conserved Domain Database, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below.  Continue reading “Read About NCBI Resources in 2023 Nucleic Acids Research Database Issue” →