Tag: Genome Data Viewer (GDV)

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

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

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!

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!

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:

New RefSeq annotations!

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.

New RefSeq annotations!

New RefSeq annotations!

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

    • 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) 

Continue reading “New RefSeq annotations!”

Join NCBI at PAG XXIX

Join NCBI at PAG XXIX

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:

Continue reading “Join NCBI at PAG XXIX”

NCBI genome browsers: search and you will find!

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 coordinatescytogenetic bandassembly scaffold/componentdisease/phenotypedbSNP identifier, or RefSeq transcript/protein accession. We’ve gathered example searches in the table below.

Search term Example(s)
Chromosome coordinate chr1:1,500,000-2,000,000
chr2: 1.5M-2,540.2K
3: 21.335M..21.337M
3: 21.335M..21.337M
chr5
Cytogenetic band 1p36.21
2q13
Assembly scaffold NT_005403.18
NW_021159987.1
Assembly component AC106865.4
AC018680.4
Gene/protein name PTEN
protease
Disease/phenotype diabetes
eye color
SNP rsID rs863223352
dbVar ID rs863223352
RefSeq transcript/protein accession NM_017551.3
XP_011538173.1
Ensembl gene/transcript indentifier ENSG00000233258
ENST00000404547
HGVS NM_001318787.2:c.2258G>A
NP_001289617: p.Arg272Cys

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.

variation viewer search by HGVS results
Figure 1. Variation Viewer showing results of search by an HGVS pattern, NP_001289617.1: p.Arg272Cys.

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.