NCBI Insights

NCBI Insights

• NCBI Taxonomy Updates to Prokaryotes October 2, 2024
  As previously announced, NCBI is continuing to improve our Taxonomy resource. The International Code of Nomenclature of Prokaryotes (ICNP) recently introduced changes to the code of nomenclature that governs naming of prokaryotes. Following these changes, we are updating the higher-level classification of prokaryotes with the introduction of rank ‘kingdom’ a […]
  NCBI Staff
• Viewing Ligand-Protein Interactions in iCn3D September 30, 2024
  Are you interested in viewing how a protein interacts with a ligand? iCn3D, our 3D molecular structure viewer, now offers improved displays of these interactions at an atomic level.   Check out this example:  You are now able to see the interactions of an embedded ligand (such as the drug Gleevec in the protein ABL2) within … Continue reading Viewing Ligand- […]
  NCBI Staff
• Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome” September 25, 2024
  NCBI is streamlining the terminology around our reference genomes. We currently have a small set of genomes collectively called representatives and an even smaller set called references. We have slowly converged on the term reference to refer to both sets.   A genome is labeled reference if it is deemed to be the best available genome … Continue reading Upda […]
  NCBI Staff
• Access Public Reports of Foreign Contamination Screen (FCS) Tool Results September 24, 2024
  Do you use genomes from NCBI and are concerned they may contain contaminant sequences? Now you can view reports generated for all prokaryotic and eukaryotic genomes with NCBI’s quality assurance tool, Foreign Contamination Screen (FCS), to better understand possible issues that may affect your studies.   What reports are available?  Summary reports to select […]
  NCBI Staff
• Updated Bacterial and Archaeal Reference Genome Collection now Available! September 19, 2024
  Download the updated bacterial and archaeal reference genome collection! We built this collection of 20,403 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). Changes have been made to the selection criteria including upgra […]
  NCBI Staff
• RefSeq Release 226 is Available! September 17, 2024
  Check out RefSeq release 226, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets. The release is provided in several directories as a complete dataset and also divided by logical groupings. What’s included in this release? As of September 13, 2024, this full release incorporates genomic, transcript, and protein data […]
  NCBI Staff
• NCBI’s Read Assembly and Annotation Pipeline Tool (RAPT) to Retire December 2024 September 16, 2024
  As of December 2024, NCBI’s pilot tool, Read Assembly and Annotation Pipeline Tool (RAPT) will no longer be available. We encourage you to check out NCBI’s suite of assembly and annotation tools including the genome assembler SKESA, the taxonomic assignment tool ANI, and the prokaryotic genome annotation pipeline (PGAP). Stay up to date Follow us on social @ […]
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• Changes to SRA Data Access on Amazon Web Services (AWS) September 11, 2024
  Cost-effective alternatives for accessing SRA data   Important note! The storage tier for Sequence Read Archive (SRA) data available through Amazon Web Services (AWS) commercial buckets is transitioning to Infrequent Access. This change is projected to be complete by the end of September 2024. To mitigate the cost impact of this change, we recommend adjustin […]
  NCBI Staff
• Coming Soon! Improving Representation of Functional Data in ClinVar September 10, 2024
  NCBI is improving the way that functional data are submitted to ClinVar and how they are represented in the XML format and on the website. Almost half of the variants in ClinVar are variants of uncertain significance (VUS). It’s unclear what clinical action to take for these variants, creating a challenge for clinicians. One potential … Continue reading Comi […]
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• Submitting High-Throughput Sequence Data to Gene Expression Omnibus (GEO) September 4, 2024
  Submit your transcriptomic and epigenomic data to Gene Expression Omnibus (GEO)! GEO is a public functional genomics data repository that relies on your data submissions. We are pleased to announce a new submission interface to improve your experience.   What’s new?  A web interface for uploading your GEO metadata   Metadata immediately validated for format […]
  NCBI Staff