Tag: NCBI Datasets

Ortholog Groups Added for ~2 Million Insect Genes

Find evolutionarily related genes across insects and other arthropods on our new Ortholog webpages

NCBI recently released a set of orthologs for approximately 2 million insect genes. You can now find and access the orthologous genes, transcripts, and proteins by searching a species and gene name in NCBI All Databases, NCBI Gene, or NCBI Datasets. As previously described, these orthologs are based on comparisons to the Drosophila melanogaster annotated genome. Using Drosophila gene nomenclature for orthologs should lead to more informative gene symbols for insects and other arthropods. Continue reading “Ortholog Groups Added for ~2 Million Insect Genes” →

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” →

Browse Taxonomy Records with NCBI Datasets

New & improved NCBI Datasets Taxonomy pages and command-line service

NCBI Datasets is excited to introduce new features to our Taxonomy pages making it easier for you to access, browse, and download taxonomic information about organisms at any taxonomic level.

What’s new?

Explore Taxonomy records with an updated look and feel
Access and download taxonomic metadata from the web or with our updated command-line (CLI) tools

Continue reading “Browse Taxonomy Records with NCBI Datasets” →

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!” →

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” →

Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools

As part of our ongoing effort to enhance your experience, we are updating the NCBI Datasets application programming interfaces (APIs). Beginning in June 2024, the v2alpha APIs will be promoted to the stable v2 version. At this time, the v1 API, the command-line interface (CLI) version 13 and older versions, and the Python library v1 will be deprecated and thus no longer supported for bug fixes or updates. Effective December 31, 2024, these will no longer be available for use.

Our updated APIs and CLI tools include new features and functionality based on your feedback. We’re committed to making this transition as smooth as possible and encourage you to review our FAQs for more details. If you use NCBI Datasets web pages and command-line tools v14+, no action is required. Continue reading “Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools” →

New RefSeq Annotations Now Available!

During October to January, the NCBI Eukaryotic Genome Annotation Pipeline released seventy new annotations in RefSeq!

New Annotations

Alnus glutinosa (eudicot)
Amyelois transitella (moth)
Anolis sagrei ordinatus (Brown anole)
Apis cerana (Asiatic honeybee)
Balaenoptera ricei (Rice’s whale)
Bombus pascuorum (bee)
Bos javanicus (banteng)
Bos taurus (cattle)

Continue reading “New RefSeq Annotations Now Available!” →

HomoloGene Now Redirects to NCBI Datasets Gene

A new way to view and download related genes

As previously announced, HomoloGene now automatically redirects to the NCBI Datasets Gene page giving you easy access to up-to-date sequence and homology data. The NCBI Datasets Gene Table provides a link to NCBI Orthologs with expanded gene and protein information and links to tools. NCBI Orthologs includes more genes and sequences for a growing range of taxa. See an example below. Legacy HomoloGene data remains available on the FTP site. Continue reading “HomoloGene Now Redirects to NCBI Datasets Gene” →

RefSeq Release 222 Now Available!

Check out RefSeq release 222, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

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

411,137,832 records
304,562,770 proteins
59,343,570 RNAs
sequences from 145,371 organisms

Continue reading “RefSeq Release 222 Now Available!” →

Using NCBI Data and Tools for Your Research Project

Are you a biology student working on a research project? NCBI offers free access to a wide variety of resources and tools to help you find and download data for your project. 

How and why do you use our resources? Check out the example below:

Your professor has assigned you a research project looking at the sequence and structure of the TP53 gene in the domestic cat (Felis catus). In addition, you were asked to find information on this gene and its genomic region in other members of the cat family (Felidae). Continue reading “Using NCBI Data and Tools for Your Research Project” →