Tag: RefSeq

An updated bacterial and archaeal reference genome collection is available!

Download the updated bacterial and archaeal reference genome collection! We built this collection of 21,258 genomes by selecting the “best” genome assembly for each species among the 400,000+ prokaryotic genomes in RefSeq.

What’s new?

As previously announced, we updated our release process:

There is now an incremental process. In addition to quarterly releases, there will be weekly updates to create references for new species which do not have a reference genome and to correct any inconsistencies in the set of references due to taxonomic merges. As a result, there may be more frequent updates to the reference set.
There is now a history tracking file available under the ASSEMBLY_REPORTS path on FTP that lists the history of reference genome selection, including both prokaryotes and eukaryotes.

Continue reading “An updated bacterial and archaeal reference genome collection is available!” →

NCBI Resources Highlighted in 2025 Nucleic Acids Research Database Issue

The 2025 Nucleic Acids Research Database Issue features papers from NCBI staff on ClinVar, PubChem, GenBank, RefSeq, and more. The citations are available in PubMed with full-text available in PubMed Central (PMC). To read an article, click on the PMCID number listed below.

Database resources of the National Center for Biotechnology Information in 2025

PMCID: PMC11701734

NCBI provides online information resources for biology, including the GenBank® nucleic acid sequence repository and the PubMed® repository of citations and abstracts published in life science journals. NCBI is currently developing the NIH Comparative Genomics Resource (CGR) to facilitate reliable comparative genomics analyses with an NCBI Toolkit and community collaboration.

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RefSeq Release 228 is Available!

Check out RefSeq release 228, 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.

What’s included in this release?

As of January 3, 2025, this full release incorporates genomic, transcript, and protein data containing:

513,096,240 records, including
391,903,900 proteins
67,997,702 RNAs
Sequences from 162,138 organisms

Continue reading “RefSeq Release 228 is Available!” →

Now Available! NCBI Hidden Markov Models (HMM) Release 17.0

Download release 17.0 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.

What’s New?

Release 17.0 contains:

17,433 HMMs maintained by NCBI
386 new HMMs since release 16.0

Continue reading “Now Available! NCBI Hidden Markov Models (HMM) Release 17.0” →

RefSeq Release 227 is Available!

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.

What’s included in this release?

As of November 4, 2024, this full release incorporates genomic, transcript, and protein data containing:

497,549,107 records, including
377,783,847 proteins
66,987,567 RNAs
Sequences from 159,324 organisms

Continue reading “RefSeq Release 227 is Available!” →

Expansion of Ortholog Data for RefSeq Arthropods

250K+ new Hymenoptera orthologs added

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” →

Updated Genomes Terminology! “Representative Genome” is Replaced with “Reference Genome”

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”” →

Access Public Reports of Foreign Contamination Screen (FCS) Tool Results

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 better assemblies at thresholds of your choosing.
Detailed reports to remove or mask contaminant sequences so they don’t adversely affect analyses. This is particularly useful for building k-mer databases.
Individual assembly reports available through the FTP link located on NCBI Datasets genome pages.
Reports are available for all eukaryotic and prokaryotic GenBank and RefSeq assemblies, currently covering over 2.7 million assemblies.
A README to understand how to interpret and use contamination reports.

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Updated Bacterial and Archaeal Reference Genome Collection now Available!

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.

What’s New?

2,298 species have an updated reference
1,123 species are represented in this collection for the first time
1,125 species have a better reference assembly than in the April 2024 set
50 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment

Continue reading “Updated Bacterial and Archaeal Reference Genome Collection now Available!” →

RefSeq Release 226 is 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.

What’s included in this release?

As of September 13, 2024, this full release incorporates genomic, transcript, and protein data containing:

472,512,852 records
355,355,673 proteins
65,576,846 RNAs
Sequences from 155,792 organisms

Continue reading “RefSeq Release 226 is Available!” →