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? … Continue reading Using Average Nucleotide Identity (ANI) to Expose Potentially Problematic Taxonomic Merges → (Source: NCBI Insights)
Source: NCBI Insights - August 2, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news
New annotations in RefSeq!
In April, May, and June, the NCBI Eukaryotic Genome Annotation Pipeline released eighty-two new annotations in RefSeq for the following organisms: Acinonyx jubatus (cheetah) Actinidia eriantha (eudicot) Amaranthus tricolor (eudicot) Amphiprion ocellaris (clown anemonefish) Anastrepha obliqua (fly) Argiope bruennichi (spider) Balaenoptera acutorostrata (minke whale) Beta vulgaris subsp. vulgaris (beet) Betta splendens (Siamese fighting fish) Biomphalaria glabrata (bloodfluke planorb) Boleophthalmus … Continue reading New annotations in RefSeq! → (Source: NCBI Insights)
Source: NCBI Insights - July 24, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) Datasets Eukaryotic genome annotation Genome Data Viewer (GDV) RefSeq RefSeq Functional Elements Source Type: news
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 … Continue reading New and Improved SciENcv Biographical Sketch Experience Coming Soon! → (Source: NCBI Insights)
Source: NCBI Insights - July 20, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New SciENcv Source Type: news
RefSeq Release 219
RefSeq release 219 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 July 18, 2023, this full release incorporates genomic, transcript, and protein data containing: 371,291,248 records 3,752,372,037,103 nucleotide bases 106,842,615,422 amino acids sequences from 138,491 organisms The release is provided in several directories … Continue reading RefSeq Release 219 → (Source: NCBI Insights)
Source: NCBI Insights - July 18, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) RefSeq Source Type: news
dbGaP: Making it Easier to Find Study Data with Third-Party Annotations
The database of Genotypes and Phenotypes (dbGaP) is a free resource that contains human data from a variety of large-scale studies. While you can’t view individual-level data without applying for controlled access, you can easily find dbGaP studies using the dbGaP Advanced Search (see screenshot below) and quickly filter studies based on study variables, molecular … Continue reading dbGaP: Making it Easier to Find Study Data with Third-Party Annotations → (Source: NCBI Insights)
Source: NCBI Insights - July 13, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Database of Genotypes and Phenotypes (dbGaP) Source Type: news
New & Improved NCBI Datasets Genome and Assembly Pages
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 … Continue reading New & Improved NCBI Datasets Genome and Assembly Pages → (Source: NCBI Insights)
Source: NCBI Insights - July 11, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly Basic Local Alignment Search Tool (BLAST) Comparative Genomics Resource (CGR) Datasets Genome Genome Data Viewer (GDV) Source Type: news
table2asn: An Updated, More Powerful Command-Line Program
As part of our ongoing effort to enhance your experience, NCBI is excited to promote table2asn, an updated, more powerful command-line program that creates sequence records for submission to GenBank. table2asn is the replacement for the older now-obsolete tool tbl2asn, with very similar operation and additional features. The program is used most frequently to create annotated … Continue reading table2asn: An Updated, More Powerful Command-Line Program → (Source: NCBI Insights)
Source: NCBI Insights - July 6, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news
Now Available! Access to Historical Human Transcript Alignments
Do you need to work with variant data mapped to historical human RefSeq transcript versions? To make it easier to map your data to the current GRCh38 reference genome and MANE transcripts, we’re now providing a collection of RefSeq transcript alignments including both the latest versions in the GCF_000001405.40-RS_2023_03 annotation release, and older transcripts going … Continue reading Now Available! Access to Historical Human Transcript Alignments → (Source: NCBI Insights)
Source: NCBI Insights - June 29, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Genome Data Viewer (GDV) RefSeq Source Type: news
GenBank Release 256.0 is Available!
Genbank release 256.0 (6/21/2023) is now available on the NCBI FTP site. This release has 24.45 trillion bases and 3.66 billion records. The current release has: 243,560,863 traditional records containing 1,966,479,976,146 base pairs of sequence data 2,611,654,455 WGS records containing 21,791,125,594,114 base pairs of sequence data 683,922,756 bulk-oriented TSA records containing 643,127,590,034 base pairs of … Continue reading GenBank Release 256.0 is Available! → (Source: NCBI Insights)
Source: NCBI Insights - June 28, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news
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 … Continue reading NCBI Virus: Mutation-Based Search for SARS-CoV-2 Data → (Source: NCBI Insights)
Source: NCBI Insights - June 27, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank NCBI Virus SARS-CoV-2 Sequence Read Archive (SRA) Source Type: news
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 … Continue reading NCBI SARS-CoV-2 Resources Page Will Redirect Soon → (Source: NCBI Insights)
Source: NCBI Insights - June 21, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New NCBI Virus SARS-CoV-2 Source Type: news
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 … Continue reading Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI → (Source: NCBI Insights)
Source: NCBI Insights - June 15, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New BioProject Comparative Genome Viewer (CGV) Datasets GenBank Genome Data Viewer (GDV) Source Type: news
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 … Continue reading Making Discoveries in Canine & Human Oncology using the NIH Comparative Genomics Resource (CGR) → (Source: NCBI Insights)
Source: NCBI Insights - June 14, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) Source Type: news
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 … Continue reading New! May 2023 Release of Stand-Alone PGAP → (Source: NCBI Insights)
Source: NCBI Insights - June 12, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Hidden Markov Models (HMM) NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Protein Family Model Source Type: news
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 … Continue reading New! The Comparative Genome Viewer (CGV) Dot Plot → (Source: NCBI Insights)
Source: NCBI Insights - June 8, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genome Viewer (CGV) Source Type: news
