Tag: Eukaryotic genome annotation

New annotations in RefSeq!

In February and March, the NCBI Eukaryotic Genome Annotation Pipeline released forty-two new annotations in RefSeq for the organisms listed below. Additionally, interim builds for over sixty species were run during that time period to fix some issues with gene symbol assignment.

Agelaius phoeniceus (red-winged blackbird)
Anastrepha ludens (Mexican fruit fly)
Anopheles marshallii (mosquito)
Anopheles nili (mosquito)
Anoplopoma fimbria (sablefish)
Artibeus jamaicensis (Jamaican fruit-eating bat)
Bombina bombina (fire-bellied toad) Continue reading “New annotations in RefSeq!” →

RefSeq Release 217

RefSeq release 217 is 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 8, 2023, this full release incorporates genomic, transcript, and protein data, containing:

348,351,219 records
254,500,694 proteins
50,975,429 RNAs
sequences from 130,837 organisms

The release is provided in several directories as a complete dataset and divided by logical groupings. Continue reading “RefSeq Release 217” →

New annotations in RefSeq!

In December and January, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-nine new annotations in RefSeq for the following organisms:

Acinonyx jubatus (cheetah)
Anopheles cruzii (mosquito)
Anopheles moucheti (mosquito)
Bicyclus anynana (squinting bush brown)
Budorcas taxicolor (takin)
Carassius gibelio (silver crucian carp)
Citrus sinensis (sweet orange)
Crassostrea angulata (Portugese oyster)
Culex pipiens pallens (northern house mosquito)
Drosophila gunungcola (fruit fly)
Galleria mellonella (greater wax moth)
Gossypium arboreum (tree cotton)
Gossypium raimondii (Peruvian cotton)
Harpia harpyja (harpy eagle)
Hemicordylus capensis (graceful crag lizard)
Lactuca sativa (garden lettuce)
Mercenaria mercenaria (northern quahog)
Mya arenaria (softshell)
Octopus bimaculoides (California two-spot octopus)
Oncorhynchus keta (chum salmon)
Pangasianodon hypophthalmus (striped catfish)
Panonychus citri (citrus red mite)
Panthera uncia (snow leopard) (pictured)
Peromyscus californicus insignis (California mouse)
Podarcis raffonei (Aeolian wall lizard)
Populus trichocarpa (black cottonwood)
Scomber japonicus (chub mackerel)
Tympanuchus pallidicinctus (lesser prairie-chicken)
Vigna angularis (adzuki bean)

Continue reading “New annotations in RefSeq!” →

Announcing New Names for Eukaryotic Genome Annotations in RefSeq!

The RefSeq eukaryotic genome annotation pipeline (EGAP) is moving to a new annotation naming format that can be used to unambiguously reference both the genome assembly and the RefSeq annotation. This will improve clarity when reporting the data you use and make the data more FAIR (Findable, Accessible, Interoperable, and Reusable). The new naming convention applies to all eukaryotic annotations released after December 15, 2022.

Historically, RefSeq EGAP has used an integer to identify a particular annotation release, such as Homo sapiens Annotation Release 110. This method provides no information on the assembly used for the annotation. In the new RefSeq naming system, annotation releases are designated by a combination of the assembly identifier (e.g., GCF_000001405.40) and an annotation name (e.g., RS_2022_04). The annotation name consists of an RS prefix to indicate RefSeq annotation, and the year and month that it was generated, RS_YYYY_MM. You should always use the annotation name in combination with the corresponding assembly accession.version, for example, GCF_026419915.1-RS_2022_12 (as shown in Figure 1). This ensures that you’re always using the name that defines a specific annotation for a specific genome assembly. If you use only part of the name, it will be ambiguous.

Figure 1. The annotation section of the Datasets Genome page for the assembly bHarHar1 for the harpy eagle (Harpia harpyja) showing the new annotation release GCF_026419915.1-RS_2022_12. Continue reading “Announcing New Names for Eukaryotic Genome Annotations in RefSeq!” →

RefSeq Release 216

RefSeq release 216 is now available online, from the FTP site, and through NCBI’s new resource, Datasets.

This full release incorporates genomic, transcript, and protein data available as of January 9, 2023, and contains 342,395,932 records, including 249,868,639 proteins, 49,869,497 RNAs, and sequences from 128,299 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 216” →

NIH Comparative Genomics Resource project

The potential impact of emerging model organisms on human health

Comparative genomics is a science that compares genomic data either within a species or across species to answer questions in biomedicine. Laboratory experiments can then investigate the functional impact of those genomics similarities and differences. The history of comparative genomics goes back to the mid-1990s, but comparative genomics is now accelerating. A flood of new data is emerging as DNA sequencing technology becomes cheaper and commoditized. While this growth poses many challenges to current tools and approaches, it also offers immense opportunity for scientific research and understanding. These insights continue to reveal novel model organisms that can further the impact of comparative genomics on human health. Continue reading “NIH Comparative Genomics Resource project” →

New RefSeq Annotations!

In October and November, the NCBI Eukaryotic Genome Annotation Pipeline released thirty-one new annotations in RefSeq for the following organisms:

Acanthochromis polyacanthus (spiny chromis)
Acomys russatus (golden spiny mouse)
Andrographis paniculata (eudicot)
Antechinus flavipes (yellow-footed antechinus)
Apodemus sylvaticus (European woodmouse)
Apus apus (common swift)
Arachis duranensis (eudicot)
Continue reading “New RefSeq Annotations!” →

Join NCBI at PAG 30

San Diego, January 13-18, 2023

NCBI is looking forward to seeing you in person at the International Plant and Animal Genome Conference (PAG 30), January 13-18, 2023 in San Diego, California.

We’re especially excited to share our recent efforts on the NIH Comparative Genomics Resource (CGR), a multi-year National Library of Medicine (NLM) project to maximize the impact of eukaryotic research organisms and their genomic data resources on biomedical research.

We also want to hear from you! If you’re interested in sharing your feedback on your needs and experiences involving comparative genomics tools to inform CGR, consider joining our Feedback Session.

Check out NCBI’s schedule of activities and events: 

Continue reading “Join NCBI at PAG 30” →

RefSeq Release 215

RefSeq release 215 is now available online, from the FTP site and through NCBI’s Entrez programming utilities, E-utilities.

This full release incorporates genomic, transcript, and protein data available as of November 7, 2022, and contains 335,372,031 records, including 244,583,657 proteins and sequences from 125,116 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 215” →

New annotations in RefSeq!

In August and September, the NCBI Eukaryotic Genome Annotation Pipeline released thirty-eight new annotations in RefSeq for the following organisms:

Adelges cooleyi (spruce gall adelgid)
Aethina tumida (small hive beetle)
Anopheles aquasalis (mosquito)
Anopheles maculipalpis (mosquito)
Anthonomus grandis grandis (boll weevil)
Aphis gossypii (cotton aphid)
Bactrocera neohumeralis (fly)
Bombus affinis (bee)
Bombus huntii (bee)
Cataglyphis hispanica (ant)
Cygnus atratus (black swan) (pictured) Continue reading “New annotations in RefSeq!” →