Tag: Genome Data Viewer (GDV)

Now Available! Access to Historical Human Transcript Alignments

Now Available! Access to Historical Human Transcript Alignments

Do you need to work with variant data mapped to historical human RefSeq transcript versions? To make it easier to map your data to the current GRCh38 reference genome and MANE transcripts, we’re now providing a collection of RefSeq transcript alignments including both the latest versions in the GCF_000001405.40-RS_2023_03 annotation release, and older transcripts going back to 1999. The data are available for download from the FTP site.  

Example

As shown in the example below (Image 1), you can view these alignments in the Genome Data Viewer by loading the remote bam track (GCF_00001405-RS_2023_03_knownrefseqs_aln.bam) from the FTP site.   Continue reading “Now Available! Access to Historical Human Transcript Alignments” →

Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI

Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI

Have you ever wondered how your genetic make-up is different from your neighbor’s? The National Human Genome Research Institute (NHGRI)-funded Human Pangenome Research Consortium (HPRC) has built an initial version of a pangenome reference – a collection of new human reference genome sequences representing 47 individuals from across the globe. Pangenome graphs relate the sequences from the different genomes to one another. The pangenome allows researchers to compare these DNA sequences and get a more detailed view of the range of human genetic variation. This is the first step toward the HPRC’s goal of building a pangenome reference comprised of the genomes of 350 individuals from diverse genetic backgrounds.  Continue reading “Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI” →

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

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!

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.

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 [email protected] if you have any questions or concerns. 

New annotations in RefSeq!

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!

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!” →