Tag: NCBI Taxonomy

Upcoming Changes to NCBI Taxonomy Classifications

Upcoming Changes to NCBI Taxonomy Classifications

NCBI is continually making improvements to our Taxonomy resource in response to new data and changes in biological nomenclature and classification. In the coming months, we will update the higher-level classification of birds (Aves), budding yeasts (Saccharomycotina), prokaryotes (Bacteria and Archaea) and Viruses. This update will also change the formal ranks of several high-level taxonomic names including Eukaryota. Except for the new species names for Viruses, none of these changes will affect organism names at the species level or below.  

Here is a brief overview of changes to each group in the order we plan to make them. Stay tuned for upcoming posts, which will describe the changes for each category in more detail.  Continue reading “Upcoming Changes to NCBI Taxonomy Classifications” →

Now Available! Updated Bacterial and Archaeal Reference Genomes Collection

Now Available! Updated Bacterial and Archaeal Reference Genomes Collection

Download the updated bacterial and archaeal reference genome collection! We built this collection of 19,328 genomes by selecting the “best” genome assembly for each species among the 350,000+ prokaryotic genomes in RefSeq (except for E. coli for which two assemblies were selected as reference).

What’s New?
  • 413 species are represented in this collection for the first time
  • 198 species are represented by a better assembly
  • 27 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” →

Browse Taxonomy Records with NCBI Datasets

Browse Taxonomy Records with NCBI Datasets

New & improved NCBI Datasets Taxonomy pages and command-line service 

NCBI Datasets is excited to introduce new features to our Taxonomy pages making it easier for you to access, browse, and download taxonomic information about organisms at any taxonomic level.  

What’s new?
  • Explore Taxonomy records with an updated look and feel  
  • Access and download taxonomic metadata from the web or with our updated command-line (CLI) tools 

Continue reading “Browse Taxonomy Records with NCBI Datasets” →

BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024

Easily generate BLAST FASTA files yourself! 

In April 2024, the FASTA (sequence text) files of the sequences in the Basic Alignment Search Tool (BLAST) databases will no longer be available on the FTP site. However, you can easily generate FASTA files yourself from the formatted BLAST databases by using the BLAST utility blastdbcmd that comes with the standalone BLAST programs. This provides you the flexibility to generate organism-specific FASTA files using NCBI’s taxonomy IDs for specific organisms or groups.   

See the examples below and the BLAST Command Line Applications User Manual for more details on the standalone BLAST programs and working with the BLAST databases.  Continue reading “BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024” →

Updated Bacterial and Archaeal Reference Genome Collection is Available!

Updated Bacterial and Archaeal Reference Genome Collection is Available!

Download the updated bacterial and archaeal reference genome collection! This collection (18,941 genomes as of Jan 18, 2024) was built by selecting the “best” genome assembly for each species among the 330,000+ prokaryotic genomes in RefSeq (except for E. coli for which two assemblies were selected as reference). You can speed up your sequence searches by running them against these high-quality genomes instead of the entire nucleotide or protein database.

The criteria for selecting the reference assembly for a given species include assembly contiguity and completeness and quality of the RefSeq annotation. Continue reading “Updated Bacterial and Archaeal Reference Genome Collection is Available!” →

Using NCBI Data and Tools for Your Research Project

Using NCBI Data and Tools for Your Research Project

Are you a biology student working on a research project? NCBI offers free access to a wide variety of resources and tools to help you find and download data for your project.  

How and why do you use our resources? Check out the example below:

Your professor has assigned you a research project looking at the sequence and structure of the TP53 gene in the domestic cat (Felis catus). In addition, you were asked to find information on this gene and its genomic region in other members of the cat family (Felidae).  Continue reading “Using NCBI Data and Tools for Your Research Project” →

Now Available! Updated Bacterial and Archaeal Reference Genomes Collection

Now Available! Updated Bacterial and Archaeal Reference Genomes Collection

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. 

What’s new?
  • 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” →

Important Update! Changes to ASSEMBLY_REPORTS and GENOME_REPORTS on FTP

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” →

Join NCBI at ASM Microbe 2023

Join NCBI at ASM Microbe 2023

Houston, TX, June 15-19, 2023

NCBI is looking forward to seeing you in person at the American Society for Microbiology Annual Meeting (ASM Microbe 2023). NCBI staff will participate in a variety of activities and events and will also be available at our booth (#2410) to address your questions. We’re especially excited to share our recent efforts on the NCBI Pathogen Detection Project which integrates bacterial and fungal pathogen genomic sequences from numerous ongoing foodborne illness and environmental surveillance and research efforts. 

Check out our schedule of activities and events below (and on our conference webpage). All times are in CST.  Continue reading “Join NCBI at ASM Microbe 2023” →

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: