- 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)
Tag: Genome Data Viewer (GDV)
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!”
- 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.
- Aegilops tauschii (monocot)
- Camelus bactrianus (Bactrian camel)
- Colias croceus (clouded yellow)
- Echinops telfairi (small Madagascar hedgehog)
- Harmonia axyridis (beetle)
- Lemur catta (Ring-tailed lemur)
- Leopardus geoffroyi (Geoffroy’s cat)
- Macaca fascicularis (crab-eating macaque)
- Maniola jurtina (meadow brown)
- Meles meles (Eurasian badger)
- Melitaea cinxia (Glanville fritillary) (pictured)
Announcing a new feature in NCBI Datasets: the gene table.
Figure 1: Human species page. Click “View all genes” to view a table of human genes.
Introducing the NIH Comparative Genomics Resource (CGR)
NCBI is looking forward to seeing you in person at the International Plant and Animal Genome Conference (PAG XXIX), January 8-12, 2022 in San Diego, California. We’re especially excited to introduce our newest endeavor – the NLM initiative known as the NIH Comparative Genomics Resource (CGR)– a platform we are developing to support comparative analyses of sequenced eukaryotic research organisms. Understanding and supporting the needs of researchers is a fundamental element in the development of CGR and is critical to its future success in supporting a large and diverse collection.
Please join NCBI for the following events to learn more about CGR and how you can inform its development:
If you’ve ever tried searching for a genomic location in NCBI’s Genome Data Viewer (GDV) or Variation Viewer and found that your search term didn’t work, it’s time to try again! We recently expanded support for searches in our genome browsers using non-NCBI identifiers such as HGVS patterns (e.g. NM_001318787.2:c.2258G>A) and Ensembl IDs. You can also search by chromosome coordinates, cytogenetic band, assembly scaffold/component, disease/phenotype, dbSNP identifier, or RefSeq transcript/protein accession. We’ve gathered example searches in the table below.
|RefSeq transcript/protein accession||NM_017551.3
|Ensembl gene/transcript indentifier||ENSG00000233258
When you search by single coordinate, SNP or dbVar ID, or HGVS, the browser view zooms to the location of the search result. A marker is automatically created to identify the searched position. For HGVS, the marker is labelled with the corresponding rsID, if there is one.
As always, please contact us if you have additional questions or suggestions about this or any other feature in GDV or Variation Viewer. You can use the Feedback button on the page or write to the NCBI Help Desk directly.
NCBI’s Genome Data Viewer (GDV) now supports visualization and analysis of nearly 400 submitter-annotated chromosome-level assemblies from the INSDC (GenBank/ENA/DDBJ). These submitter-annotated assemblies join more than 1,200 NCBI RefSeq-annotated assemblies available in GDV for hundreds of eukaryotes, spanning fungi, plants, fish, insects, and all major model organisms.
Figure 1. Submitter-annotated Malus domestica (apple) assembly displayed in GDV. GDV provides submitter-provided gene annotation, as well as some additional tracks including interspersed repeats identified by RepeatMasker and six-frame translations (not shown). Red boxes indicate useful tools and panels including a search box, an exon navigator, and interfaces to add user data and conduct NCBI BLAST searches.
The Genome Data Viewer (GDV) is now the comprehensive NCBI genome browser. The development of GDV led to a few different types of genome browsers along the way, each one originally delivering visual displays for particular datasets. We developed the 1000 Genomes Browser for variation data from the 1000 Genomes project, the dbGaP Data Browser for controlled-access sequence read alignment data, and the GeT-RM browser for Genome in a Bottle (GIAB) data.
The data displayed in these three browsers is now either obsolete and/or can largely be accessed from the GDV browser or other NCBI resources. Moreover, unlike GDV, these older browsers are no longer under active development and the data has not been updated to meet changing needs of the communities they were developed to serve. For these reasons we will retire these browsers in April 2022. Please see details below for more information on the data displayed in these browsers and how to access and display these data now through GDV and other means.