Sequence data from the ongoing avian influenza A (H5N1) virus outbreak in cattle are now available through NLM’s NCBI resources NCBI Virus and NCBI Datasets.
These data were submitted by the U.S. Department of Agriculture (USDA), U.S. Centers for Disease Control and Prevention (CDC), the World Health Organization (WHO), Iowa State University, and St. Jude Children’s Research Hospital. Continue reading “New Data Available! Access Avian Influenza A (H5N1) Virus Sequences at NCBI”
NCBI recently released a set of orthologs for approximately 2 million insect genes. You can now find and access the orthologous genes, transcripts, and proteins by searching a species and gene name in NCBI All Databases, NCBI Gene, or NCBI Datasets. As previously described, these orthologs are based on comparisons to the Drosophila melanogaster annotated genome. Using Drosophila gene nomenclature for orthologs should lead to more informative gene symbols for insects and other arthropods. Continue reading “Ortholog Groups Added for ~2 Million Insect Genes”
The National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) and other Founding Members of the International Nucleotide Database Collaboration (INSDC) have enhanced its website, www.insdc.org, to provide comprehensive information on how interested parties from around the world can evaluate their readiness to participate in the INSDC. This effort supports INSDC’s aim to broaden membership and attract qualified nucleotide sequence databases. Web content now includes a formalized Founders Arrangement and a Membership Arrangement, along with other updated information about the INSDC mission, vision, governance, and technical documentation. In doing so, INSDC encourages interested parties to visit the INSDC website to learn more. Continue reading “International Nucleotide Database Collaboration (INSDC) Introduces Enhanced Website”
Check out RefSeq release 224, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.
As of May 6, 2024, this full release incorporates genomic, transcript, and protein data containing:
The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “New! RefSeq Release 224”
We are happy to announce the release of a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP).
Recently, NCBI Virus SARS-CoV-2 Variants Overview moved from a manual to an automated process for selecting mutations required to define a lineage (e.g., Omicron, BA.2, JN.1, etc.). With this update, the SARS-CoV-2 Variant Overview provides coverage for all SARS-CoV-2 lineages and is no longer limited to only lineages with CDC status. The SARS-CoV-2 Variants Overview website reports results from analyzing both GenBank and unassembled Sequence Read Archive (SRA) sequence data. It allows you to view geographic and frequency trends of records assigned to Pango lineages and search for sequence records using lineage-defining or other mutations (example shown in Figure 1). Continue reading “Automated Lineage Definitions Now Available in NCBI Virus SARS-CoV-2 Variants Overview”
Have you ever wanted to compare antibiotic resistance data and resistance gene calls in bacteria? Now you can! Easily access and browse antibiotic susceptibility testing (AST) data and link to other NCBI resources using the new AST Browser. NCBI has collected AST data for many isolates in the Pathogen Detection system.
Continue reading “NCBI Pathogen Detection Presents the Antibiotic Susceptibility Test (AST) Browser”
GenBank release 260.0 (4/19/2024) is now available on the NCBI FTP site. This release has 31.18 trillion bases and 4.46 billion records.
The current release has:
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).
Continue reading “Now Available! Updated Bacterial and Archaeal Reference Genomes Collection”
Download release 15.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP)! Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
Release 15.0 contains:
Continue reading “NCBI Hidden Markov Models (HMM) Release 15.0 Now Available!”