New version now available
Do you use NCBI’s standalone BLAST tool (BLAST+)? The latest version of BLAST+ is now available and includes two exciting new features! You can now run searches faster and focus your searches by organism more easily. Continue reading “Faster and Focused Searches with BLAST+ 2.15.0”
Using the NIH Comparative Genomics Resource (CGR) to gain knowledge about less-researched organisms
The scientific community relies heavily on model organism research to gain knowledge and make discoveries. However, focusing solely on these species misses valuable variation. Comparative genomics allows us to use knowledge from a model species, such as Saccharomyces cerevisiae, to understand traits in other, related organisms, such as Saccharomyces pastorianus or Saccharomyces eubayanus. Applying this information may provide valuable insight for other less-researched organisms. 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 do just that. Continue reading “Comparing Yeast Species Used in Beer Brewing and Bread Making”
Now available! You can download the ClusteredNR protein database, previously only available on the BLAST web application. As recently introduced, our ClusteredNR database allows you to get quicker BLAST results and access to information about the distribution of your hits across a wider range of organisms and evolutionary distances. The package includes the ClusteredNR BLAST database, an SQLite3 database, and several scripts for accessing cluster information and members.
Features & Benefits
- Reduced redundancy
- Faster searches
- More diverse proteins and organisms in your BLAST results
Continue reading “BLAST ClusteredNR Database is Now Available for Download!”
An updated bacterial and archaeal reference genome collection is available! This collection of 18,343 genomes was built by selecting exactly one genome assembly for each species among the 312,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.
The criteria for selecting the reference assembly for a given species include assembly contiguity and completeness and quality of the RefSeq annotation.
- 790 species were added to the collection
- 199 species are represented by a better assembly (compared to the April 2023 release)
- 70 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment
Continue reading “Now Available! Updated Bacterial and Archaeal Reference Genomes Collection”
Using the NIH Comparative Genomics Resource (CGR) to understand susceptibility to SARS-CoV-2 and other infections
Are you conducting research on animal-mediated transmission of human viral infections, such as COVID-19? 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 with comparative genomics analysis for eukaryotic genes, such as Angiotensin-converting enzyme 2 (ACE2) which is targeted by SARS-CoV-2.
NCBI resources have been beneficial in helping the scientific community understand viral infections associated with public health crises, such as COVID-19 and Influenza, and can be used for study of emerging viruses that may represent new threats. Continue reading “Which animals can catch and transmit human viral infections?”
Legacy pages now redirect
Effective July 10, 2023, NCBI’s Assembly and Genome record pages now redirect to new NCBI Datasets pages. As previously announced, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.
The following pages have been updated:
- The NCBI Assembly record pages now redirect to the new NCBI Datasets Genome record pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST.
- The NCBI Genome record pages now redirect to the NCBI Datasets Taxonomy record pages that provide a taxonomy-focused portal to genes, genomes, and additional NCBI resources.
During this transition, you will have the option to return to the legacy Genome and Assembly record pages. We will remove the legacy pages in early 2024. Continue reading “New & Improved NCBI Datasets Genome and Assembly Pages “
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)”
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”
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”
As previously announced, we are continuously curating a better Prokaryotic Reference Genomes Collection. An updated bacterial and archaeal reference genome collection is now available! This collection of 17,623 genomes was built by selecting exactly one genome assembly for each species among the 283,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.
- 480 species were added to this collection
- 178 species are represented by a better assembly
- 17 species were removed due to changes in NCBI Taxonomy or uncertainty in their species assignment
Continue reading “New Release! Updated Bacterial and Archaeal Reference Genomes Collection Now Available”