New! Introducing the Multiple Comparative Genome Viewer (MCGV) Beta Release

New! Introducing the Multiple Comparative Genome Viewer (MCGV) Beta Release

NLM’s NCBI is excited to introduce the Multiple Comparative Genome Viewer (MCGV), a new tool in active development that allows you to visualize an alignment of multiple eukaryotic genomes. While our existing Comparative Genome Viewer (CGV) allows you to compare pairs of eukaryotic assemblies, the new MCGV tool can help you analyze multiple assemblies in a single view.  

MCGV displays are based on multiple whole genome sequence alignments. You can navigate these alignments in the viewer to track evolutionarily related regions across strains or species. Focus in on a particular genome region to investigate how differences in genome structure may have contributed to differences in gene sequence and function. You can access MCGV by clicking on the “Visualize gene across species” link via the gene search results page.   Continue reading “New! Introducing the Multiple Comparative Genome Viewer (MCGV) Beta Release” →

An updated bacterial and archaeal reference genome collection is available!

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:

  1. 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.
  2. 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

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.

Continue reading “NCBI Resources Highlighted in 2025 Nucleic Acids Research Database Issue” →

RefSeq Release 228 is Available!

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!” →

Access Avian Influenza A (H5N1) Virus Sequences from the Current Outbreak at NCBI

Access Avian Influenza A (H5N1) Virus Sequences from the Current Outbreak at NCBI

The U.S. Centers for Disease Control and Prevention (CDC) has been monitoring the ongoing outbreak of the avian influenza A (H5N1) virus. This is widespread globally in wild birds, and has led to sporadic outbreaks in poultry, cows, several species of wild animals, and has been detected in exposed humans. The CDC recently sequenced the H5N1 virus in two respiratory specimens collected from a U.S. patient who was severely ill and has now died (PQ809549-PQ809564).  

As previously announced, the GenBank sequences, annotations, and metadata including from this patient are available through NLM’s NCBI resources.  Continue reading “Access Avian Influenza A (H5N1) Virus Sequences from the Current Outbreak at NCBI” →

GenBank Release 264.0 Now Available!

GenBank Release 264.0 Now Available!

GenBank release 264.0 (12/19/2024) is now available on the NCBI FTP site. This release has 38.97 trillion bases and 5.36 billion records.

The current release has: 

  • 254,365,075 traditional records containing 5,085,904,976,338 base pairs of sequence data
  • 3,957,195,833 WGS records containing 32,983,029,087,303 base pairs of sequence data
  • 957,403,887 bulk-oriented TSA records containing 820,128,973,511 base pairs of sequence data
  • 187,349,466 bulk-oriented TLS records containing 77,038,271,475 base pairs of sequence data 

Continue reading “GenBank Release 264.0 Now Available!” →

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

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” →

NCBI Taxonomy: Upcoming Changes to Viruses

NCBI Taxonomy: Upcoming Changes to Viruses

To reflect changes to the International Code of Virus Classification and Nomenclature (ICVCN) made by the International Committee on Taxonomy of Viruses (ICTV), NCBI will add binomial species names to about 3000 viruses. These updates to NCBI Taxonomy are planned for spring 2025, but you can view the changes now in the ICTV’s Virus Metadata Resource. 

We recognize that the former species names like Human immunodeficiency virus 1 (HIV-1) are broadly used in public health, educational institutions, and research. To minimize the impact of this change on those who use NCBI resources, we will add the new binomial species names (e.g. Lentivirus humimdef1) while keeping the former names available in the lineage for each species. The former names will move below the new binomial species name in the taxonomy hierarchy, ensuring continuity. Examples are provided below.   Continue reading “NCBI Taxonomy: Upcoming Changes to Viruses” →

AGP Files Will No Longer be Accepted for Genome Submissions

AGP Files Will No Longer be Accepted for Genome Submissions

Effective March 2025 

Do you submit genomes to NCBI’s GenBank? Beginning March 2025, GenBank will no longer accept AGP files for genome submissions. Historically, AGP files were submitted along with contigs as necessary information for constructing assemblies. However, thanks to technology improvements, more and more whole genome shotgun (WGS) sequences submitted to NCBI are gapped assemblies (assemblies with inserted Ns for gaps).   Continue reading “AGP Files Will No Longer be Accepted for Genome Submissions” →