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” →

Which animals can catch and transmit human viral infections?

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?” →

Improvements to the Genetic Testing Registry (GTR®) Submission Portal

Thank you for your feedback!

You asked, we listened! In response to your feedback, we made improvements to the Genetic Testing Registry (GTR®) Submission Portal to streamline your submission experience.

What’s new?

Redesigned homepage for a more intuitive submission experience
New test submission page where you can add new tests, download Excel templates, upload spreadsheets, and track API submissions
One-click download of your clinical test data right from the home page
Improved navigation within the GTR submission site making it easier to move between the home page, lab record, test management tool, and test submission page
Quick access to the ‘Groups’ feature where you can manage permissions for laboratory staff who can submit data for your lab

Continue reading “Improvements to the Genetic Testing Registry (GTR®) Submission Portal” →

NCBI Hidden Markov Models (HMM) Release 13.0 Now Available!

Release 13.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available for download. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.

What’s new?

The 13.0 release contains:

16,143 HMMs maintained by NCBI
315 new HMMs since release 12.0
286 HMMs with better names, EC numbers, Gene Ontology (GO) terms, gene symbols or publications

Continue reading “NCBI Hidden Markov Models (HMM) Release 13.0 Now Available!” →

GenBank Release 257.0 is Available!

GenBank release 257.0 (8/15/2023) is now available on the NCBI FTP site. This release has 25.10 trillion bases and 3.69 billion records.

The current release has:

246,119,175 traditional records containing 2,112,058,517,945 base pairs of sequence data
2,631,493,489 WGS records containing 22,294,446,104,543 base pairs of sequence data
686,271,945 bulk-oriented TSA records containing 646,176,166,908 base pairs of sequence data
124,421,006 bulk-oriented TLS records containing 48,289,699,026 base pairs of sequence data

During the 59 days between the close dates for GenBank Releases 256.0 and 257.0, the traditional portion of GenBank grew by 145,578,541,799 base pairs and by 2,558,312 sequence records. We updated 34,840 records during that same period. We added and/or updated an average of 43,952 traditional records per day! Continue reading “GenBank Release 257.0 is Available!” →

Now Live! New and Improved SciENcv Biographical Sketch Experience

Required for NSF grant application submissions beginning October 2023

New in Science Experts Network Curriculum Vita (SciENcv)! We are excited to introduce an updated experience for the National Science Foundation (NSF) Biographical Sketch document, allowing you to submit federal grant applications quicker and easier than ever!  

Features & Benefits

Enhanced user experience with a modern look and feel  
Intuitive and easy process that helps you fill out forms correctly  
Revised navigation to reduce administrative burden  
Document preview allows you to view your document prior to certification  
Eliminates the need to repeatedly enter biographical sketch and financial document information  
Reduces the administrative burden associated with federal grant application and reporting requirements  
Allows you to describe your scientific contributions in your own words  
Document certification

Continue reading “Now Live! New and Improved SciENcv Biographical Sketch Experience “ →

NCBI at the Biodiversity Genomics Academy 2023 (BGA23)

Virtual Talks, September 14, 2023

NCBI will be presenting virtually at the Biodiversity Genomics Academy 2023 (BGA23) on September 14, 2023. Our short, interactive talks will focus on NCBI Datasets and the Comparative Genome Viewer (CGV). Both resources are part of the NIH Comparative Genomics Resource (CGR), which facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

Recordings will be made available post-event! Continue reading “NCBI at the Biodiversity Genomics Academy 2023 (BGA23)” →

Using Average Nucleotide Identity (ANI) to Expose Potentially Problematic Taxonomic Merges

Help us improve our microbial taxonomy

NCBI uses Average Nucleotide Identity (ANI) to evaluate the taxonomic classification of prokaryotic genomes submitted to GenBank. As part of this effort, we identified heterotypic synonyms that fail to match each other with high ANI, and we invite you to help us evaluate these cases.

What is Heterotypic Synonymy?

Heterotypic synonymy refers to two or more names for different taxa (such as species) that were described independently but have been subsequently merged into a single taxon. The merged taxon will generally be referred to by the oldest name. Continue reading “Using Average Nucleotide Identity (ANI) to Expose Potentially Problematic Taxonomic Merges” →

New Annotations in RefSeq!

In April, May, and June, the NCBI Eukaryotic Genome Annotation Pipeline released eighty-two new annotations in RefSeq!

Highlights:

Homo sapiens (human) T2T-CHM13v2.0 now includes many more alternative splice variants
Homo sapiens (human) GRCh38.p14 includes all transcripts from MANE v1.2, and includes over 78,000 new RefSeq Functional Element (RefSeqFE) features added since our last annotation in 2022
Mus musculus (house mouse) GRCm39 integrates curation for over 3,000 genes and 14,000 transcripts since September 2020
Rattus norvegicus (Norway rat) mRatBN7.2, including curation of over 5000 genes since our last annotation in 2021

New annotations: Continue reading “New Annotations in RefSeq!” →

New and Improved SciENcv Biographical Sketch Experience Coming Soon!

Required for NSF grant application submissions beginning October 2023

We recently introduced a new experience for the Science Experts Network Curriculum Vita (SciENcv) Current & Pending (Other) Support Forms with updated features and functionality. Beginning in August 2023, we will offer a similar updated experience for the National Science Foundation (NSF) Biographical Sketch document, too. Submit federal grant applications quicker and easier than ever! Continue reading “New and Improved SciENcv Biographical Sketch Experience Coming Soon!” →