Tag: RefSeq

NCBI Hidden Markov Models (HMM) Release 16.0 Now Available!

Download release 16.0 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 16.0 contains:

17,078 HMMs maintained by NCBI
406 new HMMs since release 15.0
The GO terms between NCBI HMMs and the corresponding Interpro entries were compared and evaluated over a substantial number of HMMs and updated (added: 307; deleted: 39; updated: 1,482).

Continue reading “NCBI Hidden Markov Models (HMM) Release 16.0 Now Available!” →

Coming Soon! Rapid Access to Influenza Data

Improved Influenza GenBank submission process

Do you submit flu sequences to GenBank? Thanks to community feedback, NCBI is excited to announce that we are improving the influenza GenBank submission process. We continue to play a key role in providing the biomedical community free and easy access to genome sequences from viruses. To further advance public health research, in the coming weeks we will begin to expedite the release of influenza data. This means you will see the rapid assignment of accession numbers and data becoming publicly accessible within hours. In addition, we will automatically process all Influenza genomes to produce standardized, consistent annotation which saves you time and benefits the researchers who find your data valuable. Continue reading “Coming Soon! Rapid Access to Influenza Data” →

Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus

NCBI Virus now offers genomes for viruses such as Influenza A by using an automated process to group segments from the same samples. We group these segments into genomes based on metadata for the sample including species, isolate name, host organism, collection date, and location. Newly released GenBank records are added daily.

Access these genome assemblies through NCBI Virus using the new “NCBI Virus Assembly” tab above the Results Table as shown below. Continue reading “Now Available: Assembled Genomes for Influenza Viruses and Improved Functionality of NCBI Virus” →

RefSeq Release 225 Now Available!

Check out RefSeq release 225, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

As of July 8, 2024, this full release incorporates genomic, transcript, and protein data containing:

448,507,905 records
334,845,613 proteins
63,542,774 RNAs
Sequences from 152,668 organisms

The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 225 Now Available!” →

New! RefSeq Release 224

Check out RefSeq release 224, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

As of May 6, 2024, this full release incorporates genomic, transcript, and protein data containing:

435,879,646 records
324,246,652 proteins
62,348,147 RNAs
Sequences from 150,742 organisms

The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “New! RefSeq Release 224” →

Now Available! Updated Bacterial and Archaeal Reference Genomes Collection

Download the updated bacterial and archaeal reference genome collection! We built this collection of 19,328 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).

What’s New?

413 species are represented in this collection for the first time
198 species are represented by a better assembly
27 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment

Continue reading “Now Available! Updated Bacterial and Archaeal Reference Genomes Collection” →

NCBI Hidden Markov Models (HMM) Release 15.0 Now Available!

Download release 15.0 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 15.0 contains:

16,667 HMMs maintained by NCBI
279 new HMMs since release 14.0
Several hundreds HMMs with better names, EC numbers, Gene Ontology (GO) terms, gene symbols, or publications.

Continue reading “NCBI Hidden Markov Models (HMM) Release 15.0 Now Available!” →

New RefSeq Annotations Now Available!

In February and March, the NCBI Eukaryotic Genome Annotation Pipeline released forty-six new annotations in RefSeq!

New Annotations

Aedes albopictus (Asian tiger mosquito)
Anolis carolinensis (green anole)
Armigeres subalbatus (mosquito)
Bacillus rossius redtenbacheri (walking stick)
Bolinopsis microptera (comb jelly)
Bombyx mori (domestic silkworm)
Bubalus kerabau (carabao)
Candoia aspera (snake)
Cavia porcellus (domestic guinea pig)
Continue reading “New RefSeq Annotations Now Available!” →

Now Available: RefSeq Release 223

Check out RefSeq release 223, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

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

425,594,654 records
316,329,937 proteins
60,886,133 RNAs
sequences from 147,591 organisms

Continue reading “Now Available: RefSeq Release 223” →

Join NCBI at TAGC 2024

March 6-10 in Washington, D.C.

We look forward to seeing you in person at The Allied Genetics Conference (TAGC), March 6-10, 2024, in the Washington D.C. metro area. NCBI staff will participate in a variety of activities and events, including hosting a hands-on workshop: Exploring and downloading NCBI data with NCBI Datasets. We’re also excited to share our recent efforts on the NIH Comparative Genomics Resource (CGR) in a talk during Sunday’s Technology, Tools, and Resources session.

Check out NCBI’s schedule of activities and events:

Continue reading “Join NCBI at TAGC 2024” →