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Tag: Basic Local Alignment Search Tool (BLAST)
Download release 19.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
Release 19.0 contains:
Continue reading “Now Available! NCBI Hidden Markov Models (HMM) Release 19.0”
Download the updated bacterial and archaeal reference genome collection! We built this collection of 22,420 genomes by selecting the “best” genome assembly for each species among the 450,000+ prokaryotic genomes in RefSeq.
Continue reading “An Updated Bacterial and Archaeal Reference Genome Collection is Available!”
As we begin a new year, let’s look back at the top viewed NCBI Insights Blog posts of 2025!
In case you missed any of these, check them out: Continue reading “Top Posts of 2025: A Look at the NCBI Insights Blog”
Download the updated bacterial and archaeal reference genome collection! We built this collection of 22,082 genomes by selecting the “best” genome assembly for each species among the 440,000+ prokaryotic genomes in RefSeq.
Continue reading “An Updated Bacterial and Archaeal Reference Genome Collection is Available!”
Download the updated bacterial and archaeal reference Genome collection! We built this collection of 21,794 genomes by selecting the “best” genome assembly for each species among the 400,000+ prokaryotic genomes in RefSeq, which is 536 more than was included in the January release. Continue reading “Now Available: Updated Bacterial and Archaeal Reference Genome Collection”
We are excited to announce that the default database for protein BLAST searches will soon be the NCBI ClusteredNR database! Introduced in 2022, ClusteredNR is a collection of protein sequence clusters built from the current default database, nr. The representative sequence is chosen for each cluster, which is generally well-annotated and indicates the function of the proteins in the cluster, helping you focus on meaningful biological insights and decreasing redundant results.
Continue reading “Faster, Better Results for Protein BLAST Searches”
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.
As previously announced, we updated our release process:
Continue reading “An updated bacterial and archaeal reference genome collection is available!”
As we begin a new year, let’s look back at the top NCBI Insights Blog posts of 2024 based on number of views.
In case you missed any of these, check them out:
Continue reading “Top of 2024: A Look at the NCBI Insights Blog “
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”
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!”