Gene Expression Counts on NCBI RefSeq Eukaryotic Genomes
We’re rolling out exciting new features to NCBI RefSeq’s Eukaryote Genome Annotation Pipeline (EGAP)! Now you can get a better understanding of gene expression observed in different RNA-seq datasets with our newly added gene expression counts. These are determined using featureCounts based on the EGAP-produced RefSeq annotation and the set of RNA-seq runs aligned with … Continue reading Gene Expression Counts on NCBI RefSeq Eukaryotic Genomes → (Source: NCBI Insights)
Source: NCBI Insights - November 20, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news
Gene Ontology (GO) Terms for NCBI RefSeq Eukaryotic Genomes
Are you interested in more functional information about protein-coding genes? We’ve expanded NCBI RefSeq’s Eukaryote Genome Annotation Pipeline (EGAP) to include Gene Ontology (GO) terms computed for most protein-coding genes. We are using the latest version of InterProScan, which now includes analysis based on PANTHER reference trees, on all NCBI RefSeq eukaryotic genomes. That means having … Continue reading Gene Ontology (GO) Terms for NCBI RefSeq Eukaryotic Genomes → (Source: NCBI Insights)
Source: NCBI Insights - November 15, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) Eukaryotic genome annotation Gene Ontology (GO) RefSeq Source Type: news
RefSeq Release 221
RefSeq release 221 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 November 6, 2023, this full release incorporates genomic, transcript, and protein data containing: 404,657,610 records 300,054,945 proteins 57,882,313 RNAs sequences from 143,819 organisms The release is provided in several directories as a … Continue reading RefSeq Release 221 → (Source: NCBI Insights)
Source: NCBI Insights - November 14, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) Eukaryotic genome annotation Human genome NCBI Datasets RefSeq Source Type: news
NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype
Using the Pathogen Detection pipeline, we recently found new Shiga toxin 2 (stx2) subtypes in isolates from the United States collected as part of the Centers for Disease Control and Prevention (CDC) routine disease surveillance. Our pipeline relies on AMRFinderPlus to identify anti-microbial resistance (AMR), stress-resistance, and virulence genes. We screened over 60,000 E. coli … Continue reading NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype → (Source: NCBI Insights)
Source: NCBI Insights - November 9, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New NCBI Pathogen Detection PubMed Central (PMC) Source Type: news
Now Available! Compare NCBI RefSeq and UniProt Datasets
Do you need to compare and combine data based on NCBI RefSeq and UniProt datasets, and aren’t sure which proteins are comparable? For many years, NCBI Gene has provided information about the relationships between RefSeq and UniProt accessions courtesy of data imported from UniProt, but the tremendous growth of both datasets has led to large … Continue reading Now Available! Compare NCBI RefSeq and UniProt Datasets → (Source: NCBI Insights)
Source: NCBI Insights - November 8, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) Gene RefSeq Source Type: news
GenBank Release 258.0 is Available!
GenBank release 258.0 (11/2/2023) is now available on the NCBI FTP site. This release has 26.74 trillion bases and 3.85 billion records. The current release has: 247,777,761 traditional records containing 2,433,391,164,875 base pairs of sequence data 2,775,205,599 WGS records containing 23,600,199,887,231 base pairs of sequence data 701,336,089 bulk-oriented TSA records containing 659,924,904,311 base pairs of … Continue reading GenBank Release 258.0 is Available! → (Source: NCBI Insights)
Source: NCBI Insights - November 7, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news
Using NCBI Resources for Genotype-Based Medication Optimization
NCBI offers a variety of clinical genetic resources to help you research, diagnose, and treat diseases and conditions. You can quickly and easily access our data and tools through the Medical Genetics and Human Variation page of the NCBI website. How and why should you use our resources? Consider the example below. Your patient is … Continue reading Using NCBI Resources for Genotype-Based Medication Optimization → (Source: NCBI Insights)
Source: NCBI Insights - November 1, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New ClinVar Database of Genotypes and Phenotypes (dbGaP) Genetic Testing Registry (GTR) MedGen Medical Genetic Summaries (MGS) Medical genetics Single Nucleotide Polymorphism Database (dbSNP) Source Type: news
New Annotations in RefSeq!
In July, August, and September, the NCBI Eukaryotic Genome Annotation Pipeline released fifty-six new annotations in RefSeq! New Annotations Achroia grisella (moth) Acipenser ruthenus (sterlet) Ahaetulla prasina (snake) Alligator mississippiensis (American alligator) Ammospiza caudacuta (bird) Ammospiza nelsoni (bird) Anopheles bellator (mosquito) Anopheles coustani (mosquito) Anopheles ziemanni (mosquito) Arachis stenosperma (eudicot) Carassius carassius (crucian carp) Centropristis striata (black seabass) … Continue reading New Annotations in RefSeq! → (Source: NCBI Insights)
Source: NCBI Insights - October 24, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) Eukaryotic genome annotation Genome Data Viewer (GDV) NCBI Datasets RefSeq Source Type: news
Upcoming Changes to Virus Data Resources at NCBI
Effective May 2024, NCBI Virus will replace legacy virus web resources Coming soon! As part of our ongoing effort to enhance your experience and modernize our services, several of our legacy virus-related web resources will be replaced by NCBI Virus – our community portal for viral sequence data. NCBI Virus is more comprehensive, modernized, and … Continue reading Upcoming Changes to Virus Data Resources at NCBI → (Source: NCBI Insights)
Source: NCBI Insights - October 19, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Multiple Sequence Alignment Viewer (MSAV) NCBI Virus RefSeq Source Type: news
NCBI Datasets: Easily Access and Download Sequence Data and Metadata
Effective May 2024, NCBI Datasets will replace legacy Genome and Assembly web resources As part of our ongoing effort to enhance your experience and modernize our services, NCBI will gradually replace the legacy Genome and Assembly resources with the newly introduced NCBI Datasets resource. NCBI Datasets is a continually evolving platform designed to provide easy and intuitive … Continue reading NCBI Datasets: Easily Access and Download Sequence Data and Metadata → (Source: NCBI Insights)
Source: NCBI Insights - October 18, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly Comparative Genomics Resource (CGR) Genome NCBI Datasets Source Type: news
Introducing the New NCBI Datasets Genome Annotation Table
As part of our ongoing effort to modernize and improve your experience, we are excited to introduce the new NCBI Datasets genome annotation table. You can now quickly and easily access annotated gene and protein sequences annotated by NCBI RefSeq or GenBank submitters. Features & Benefits Easier than ever to search and download data for … Continue reading Introducing the New NCBI Datasets Genome Annotation Table → (Source: NCBI Insights)
Source: NCBI Insights - October 10, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) GenBank NCBI Datasets RefSeq Source Type: news
Comparing Yeast Species Used in Beer Brewing and Bread Making
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 … Continue reading Comparing Yeast Species Used in Beer Brewing and Bread Making → (Source: NCBI Insights)
Source: NCBI Insights - September 29, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Comparative Genome Viewer (CGV) Comparative Genomics Resource (CGR) Conserved Domains Database (CDD) Datasets Genome Data Viewer (GDV) Multiple Sequence Alignment Viewer (MSAV) RefSeq Source Type: news
Join NCBI at ASHG 2023
November 1-5 in Washington, D.C. We look forward to seeing you in person at the American Society for Human Genetics Annual Meeting (ASHG 2023), November 1-5, 2023, in Washington, D.C. We will participate in a variety of activities and events including hosting an exhibit booth where you can stop by to meet NCBI experts, ask questions, provide feedback, … Continue reading Join NCBI at ASHG 2023 → (Source: NCBI Insights)
Source: NCBI Insights - September 27, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New ClinVar Comparative Genomics Resource (CGR) Human genome Matched Annotation from NCBI and EMBL-EBI (MANE) RefSeq Functional Elements Single Nucleotide Polymorphism Database (dbSNP) Source Type: news
BLAST ClusteredNR Database is Now Available for Download!
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 … Continue reading BLAST ClusteredNR Database is Now Available for Download! → (Source: NCBI Insights)
Source: NCBI Insights - September 26, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) ClusteredNR Comparative Genomics Resource (CGR) Source Type: news
Successful NCBI-NIAID Codeathon Explored VCF Files in Population Genomics
Variant Call Format (VCF) files provide a crucial way to record and share information about genetic variants across samples. NCBI joined forces with the National Institute of Allergy and Infectious Diseases (NIAID) to co-host the VCF Files for Population Genomics Codeathon (July 31 – August 4). The codeathon focused on innovative methods for harnessing VCF … Continue reading Successful NCBI-NIAID Codeathon Explored VCF Files in Population Genomics → (Source: NCBI Insights)
Source: NCBI Insights - September 21, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Codeathon Genomics SARS-CoV-2 Source Type: news
