Tag: Genome Data Viewer (GDV)

Revolutionize your research with the NIH Comparative Genomics Resource (CGR)

Unlock the full potential of eukaryotic research organisms and their genomic data with the National Institutes of Health (NIH) Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses through community collaboration as well as an NCBI toolkit of interconnected, interoperable data and tools.  

Comparative genomics is a field of study that uses the genomes of many different organisms to help us understand basic biological processes and human disease. NCBI is developing CGR to help researchers take full advantage of the rapidly growing number of eukaryotic organisms that, due to recent technological advances, now have sequenced genomes and associated data that can be used in these types of studies. Its NCBI toolkit offers new and modern resources for such analyses, and its emphasis on community collaboration brings new opportunities to share and connect data. Continue reading “Revolutionize your research with the NIH Comparative Genomics Resource (CGR)” →

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!” →

NCBI’s Genome Decoration Page (GDP) to Retire in September 2023

As of September 2023, NCBI’s Genome Decoration Page (GDP) will no longer be available. Due to low usage of GDP, we are focusing our development efforts on our more popular resources and tools.

If you are using GDP to view your data mapped to genomes, we encourage you to check out our Genome Data Viewer (GDV) if you haven’t already. You can upload your data for display in GDV and export PDF or SVG images of your view.

Stay up to date 

Follow us on Twitter @NCBI and join our mailing list to keep up to date with our visualization tools and other NCBI news.  

Questions?

Feel free to contact our help desk at info@ncbi.nlm.nih.gov if you have any questions or concerns.

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!” →

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!” →

Connect with NCBI at ASHG 2022

Join us October 25-29 in Los Angeles, CA

We are looking forward to seeing you in-person at the American Society of Human Genetics (ASHG) annual meeting, October 25-29, 2022, in Los Angeles, California.

We will present a variety of talks and posters featuring our clinical and human genetic resources, as well as genome products and tools. We are excited to introduce 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 to biomedical research. If you’re interested in providing feedback that will be used to help drive CGR forward, consider joining our round table discussion.

Check out NCBI’s schedule of activities and events:

Continue reading “Connect with NCBI at ASHG 2022” →

New annotations in RefSeq

In June and July, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-six new annotations in RefSeq for the following organisms:

Anopheles coluzzii (mosquito)
Anopheles funestus (African malaria mosquito)
Astyanax mexicanus (Mexican tetra)
Athalia rosae (coleseed sawfly)
Bactrocera dorsalis (oriental fruit fly)
Brassica napus (rape)
Brienomyrus brachyistius (bony fish)
Canis lupus dingo (dingo) (pictured)
Caretta caretta (Loggerhead turtle)
Dendroctonus ponderosae (mountain pine beetle)
Epinephelus fuscoguttatus (brown-marbled grouper)
Lagopus muta (rock ptarmigan)
Marmota marmota marmota (Alpine marmot)
Nematostella vectensis (starlet sea anemone)
Ostrea edulis (bivalve)
Panthera uncia (snow leopard)
Plutella xylostella (diamondback moth)
Pyrus x bretschneideri (Chinese white pear)
Rhincodon typus (whale shark)
Rhipicephalus sanguineus (brown dog tick)
Solanum stenotomum (eudicot)
Solanum verrucosum (eudicot)
Sphaerodactylus townsendi (lizard)
Stegostoma fasciatum (shark)
Triticum urartu (monocot)
Ziziphus jujuba (common jujube)

Continue reading “New annotations in RefSeq” →

Introducing NLM’s new NCBI Datasets genome page!

As part of an ongoing effort to modernize and improve your experience, NLM’s NCBI Datasets is introducing all-new genome pages. These pages make it easier for you to browse and download genome sequence and metadata, and navigate to tools such as the Genome Data Viewer (GDV) and BLAST.

To get started, search NCBI Datasets by assembly accession (e.g., GCF_016699485.2), assembly name (e.g., bGalGal1.mat.broiler.GRCg7b), WGS accession (e.g., JAENSK01), or species name + genome (e.g., chicken genome), and click on the title in the box. See the top red arrow in Figure 1 below where we search for ‘chicken genome’.

Figure 1: Finding the chicken reference assembly. A search for ‘chicken genome’ returns a box that provides a quick link to the new genome page (middle red arrow). From there, the download button (bottom red arrow) allows you to select the files you need (see ‘Download Package’ window on the left) along with a detailed metadata report that includes all the metadata on the web page. Continue reading “Introducing NLM’s new NCBI Datasets genome page!” →

New RefSeq annotations are available!

In April and May, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-eight new annotations in RefSeq for the following organisms:

Alosa alosa (allis shad) GCF_017589495.1
Anser cygnoides (Swan goose) GCF_002166845.1
Bombus terrestris (buff-tailed bumblebee) GCF_910591885.1
Corvus hawaiiensis (hawaiian crow) GCF_020740725.1
Equus quagga (plains zebra) GCF_021613505.1 Continue reading “New RefSeq annotations are available!” →

New RefSeq annotations!

In February and March, the NCBI Eukaryotic Genome Annotation Pipeline released thirty-seven new annotations in RefSeq for the following organisms:

Belonocnema kinseyi (wasp)
Daphnia pulex (common water flea)
Daphnia pulicaria (crustacean)
Dermatophagoides farinae (American house dust mite)
Diprion similis (hymenopteran)
Drosophila willistoni (fly)
Equus quagga burchellii (Burchell’s zebra) (pictured)
Gallus gallus (chicken)
Haliotis rubra (blacklip abalone)
Haliotis rufescens (red abalone)
Helicoverpa zea (corn earworm)
Homalodisca vitripennis (glassy-winged sharpshooter)
Hydra vulgaris (swiftwater hydra)
Hypomesus transpacificus (delta smelt)
Ictalurus punctatus (channel catfish)
Ischnura elegans (damselfly)
Lolium rigidum (monocot)
Lucilia cuprina (Australian sheep blowfly)
Lynx rufus (bobcat)
Marmota monax (woodchuck)
Meles meles (Eurasian badger)
Micropterus dolomieu (smallmouth bass)
Neodiprion fabricii (hymenopteran)
Neodiprion lecontei (redheaded pine sawfly)
Neodiprion pinetum (white pine sawfly)
Neodiprion virginiana (hymenopteran)
Oncorhynchus gorbuscha (pink salmon)
Osmia bicornis bicornis (red mason bee)
Scatophagus argus (bony fish)
Schistocerca americana (American grasshopper)
Schistocerca piceifrons (Central American locust)
Silurus meridionalis (bony fish)
Ursus americanus (American black bear)
Vanessa cardui (painted lady)
Vespa crabro (European hornet)
Vigna umbellata (eudicot)
Xenia sp. Carnegie-2017 (soft coral)

View the full list of annotated eukaryotes available in the Genome Data Viewer (GDV) browser.