Tag: Eukaryotic genome annotation

Gapless Telomere to Telomere human genome (T2T-CHM13) now available

Gapless Telomere to Telomere human genome (T2T-CHM13) now available

On April 1, 2022, Science published the first complete sequence of a human genome, known as T2T-CHM13. This notable scientific achievement comes two decades after the first human genome release from the Human Genome Project and offers an in situ look at biologically important regions, such as centromeres, telomeres, and segmental duplications, that were previously unassembled. Read on to learn more about how you can access this assembly and related resources at NCBI, or to access any one of the more than 1000 human genome assemblies now in GenBank. Continue reading “Gapless Telomere to Telomere human genome (T2T-CHM13) now available”

RefSeq Release 212 is available!

RefSeq Release 212 is available!

RefSeq Release 212 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 May 2, 2022, and contains 314,915,153 records, including 229,417,182 proteins, 44,805,833 RNAs, and sequences from 119,373 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

Human genome Annotation Release 110

Annotation Release 110 is the first new annotation of human in four years, including all latest curated RefSeqs, and recalculation of models using over 80M long reads and 9B Illumina RNA-seq reads. AR 110 includes annotation of two human assemblies: Continue reading “RefSeq Release 212 is available!”

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!”

RefSeq Release 210 is available

RefSeq Release 210 is available

RefSeq Release 210 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 January 3, 2022, and contains 302,482,881 records, including 220,595,192 proteins, 42,453,222 transcripts, and sequences from 115,929 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 210 is available”

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”

New annotations in RefSeq

New annotations in RefSeq

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

  • Acropora millepora (stony coral)
  • Bubalus bubalis (water buffalo)
  • Bufo gargarizans (Asiatic toad)
  • Chrysoperla carnea (insect) (pictured)
  • Coccinella septempunctata (seven-spotted ladybird)
  • Coregonus clupeaformis (lake whitefish)
  • Cotesia glomerata (wasp)
  • Daphnia magna (crustacean)
  • Desmodus rotundus (common vampire bat)
  • Drosophila ananassae (fly)
  • Drosophila rhopaloa (fly)
  • Drosophila simulans (fly)
  • Drosophila takahashii (fly)
  • Equus asinus (ass)
  • Felis catus (domestic cat)
  • Gracilinanus agilis (agile gracile mouse opossum)
  • Homo sapiens (human)
  • Hordeum vulgare subsp. vulgare (domesticated barley)
  • Jaculus jaculus (lesser Egyptian jerboa)
  • Mangifera indica (mango)
  • Mauremys mutica (yellowpond turtle)
  • Mustela putorius furo (domestic ferret)
  • Neomonachus schauinslandi (Hawaiian monk seal)
  • Neovison vison (American mink)
  • Thunnus albacares (yellowfin tuna)
  • Tribolium madens (black flour beetle)
  • Triticum aestivum (bread wheat)
  • Ursus arctos horribilis (brown bear)
  • Varanus komodoensis (Komodo dragon)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

Save the Date: NCBI at Plant and Animal Genome (PAGXXIX), Jan 2022

Save the Date: NCBI at Plant and Animal Genome (PAGXXIX), Jan 2022

Come see NCBI in person at the International Plant and Animal Genome (PAG) Conference (PAGXXIX), January 9-12 in San Diego, California. Learn about new ways that we are supporting the data management and analysis needs of scientists working across the tree of life. We’re excited to be back after a year of unprecedented circumstances!

As we described in our NLM Director’s featured blog articles, A Journey to Spur Innovation and Discover and Using Comparative Genomics to Advance Scientific Discoveries, NCBI has recently embarked on the NIH-supported NLM initiative known as the NIH Comparative Genomics Resource (CGR). This initiative will modernize resources and infrastructure in order to promote comparative genomic analyses for all eukaryotic organisms. CGR will connect common data elements for genomic-related content with standard structures and mechanisms that will help you uncover previously unrecognized relationships. It will also provide tools that promote the quality of genomic-related data in sequence archives.

When you are at PAG, please check out our NCBI workshops and other sessions, swing by our booth, and visit our posters to learn more about ongoing CGR-related developments and additional NCBI resources related to your genomic research. We especially invite you to join our CGR Listening Session where you can offer valuable input on how NCBI can best provide a resource to support your analyses.

As PAG nears, stay tuned for more details and upcoming announcements from NCBI!

RefSeq Release 209 is available

RefSeq Release 209 is available

RefSeq release 209 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 1, 2021, and contains 296,293,486 records, including 215,655,378 proteins, 41,751,205 RNAs, and sequences from 114,396 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 209 is available”