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Tag: NCBI Datasets
Check out RefSeq release 227, 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 as divided by logical groupings.
As of November 4, 2024, this full release incorporates genomic, transcript, and protein data containing:
NCBI is excited to announce the expansion of ortholog data for RefSeq arthropods. This update expands the breadth of arthropod orthology information, offering new insights into evolutionary biology, gene function, and shared pathways. Whether you’re studying insect genetics, developmental biology, or comparative genomics, the expanded ortholog data opens up new possibilities for research. Check out our previous blog to learn how to access the orthologs using NCBI Datasets. Continue reading “Expansion of Ortholog Data for RefSeq Arthropods”
Do you use the NCBI Datasets command-line tools or API? As of January 2025, you will have the option to use an API key to increase your rate of access. This update will provide you more flexibility and efficiency, while still maintaining robust access for everyone. Note that these changes will not affect web users.
Without an API Key: You will be limited to 5 requests per second.
With an API Key: You will be able to make 10 requests per second. Continue reading “New API Key System Coming Soon to NCBI Datasets”
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’ and other changes for this group. The changes will first appear both in our legacy and new NCBI Datasets taxonomy browsers, followed by data records. This update affects every prokaryotic record and may impact some pipelines and tools using lineage and/or name recognition. Continue reading “NCBI Taxonomy Updates to Prokaryotes”
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 for the species based on assembly, annotation metrics (when available), and, in a small number of cases, curatorial review. The set of eukaryotic reference assemblies is updated continuously as new assemblies are submitted to GenBank. The set of prokaryotic references are recalculated three times a year.
Important Note: Classification of “reference genome” is separate from inclusion in RefSeq – while genomes in RefSeq are preferentially used to pick the reference genome, a reference genome can also be chosen for species not included in RefSeq. Continue reading “Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome””
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.
Continue reading “Access Public Reports of Foreign Contamination Screen (FCS) Tool Results”
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 upgrades for type and complete assemblies resulting in a much larger set of changes as compared to previous updates.
Continue reading “Updated Bacterial and Archaeal Reference Genome Collection now Available!”
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.
As of September 13, 2024, this full release incorporates genomic, transcript, and protein data containing:
As previously announced, NCBI is continually making improvements to our Taxonomy resource in response to new data and changes in biological nomenclature. We recently made classification changes to budding yeasts and allies (Saccharomycotina), which consists of more than 1,200 species and exhibits levels of genomic diversity similar to those of plants and animals. This update affects more than six million records. Check out our new Taxonomy browser in NCBI Datasets. Continue reading “NCBI Taxonomy Updates to Yeasts”
The World Health Organization (WHO) declared the recent upsurge of the mpox virus to be a public health emergency of international concern. Having timely viral genome data freely and widely available enables researchers to explore how this virus differs from viruses isolated and sequenced in the past. Therefore, NCBI’s GenBank is expediting the release of mpox data by annotating gene and coding region features as part of the submission process. Continue reading “Quick & Easy Access to Mpox Data Through NCBI Virus”