Tag: eukaryotic genome annotation

New annotations in RefSeq: budgerigar, bony fish, fly and more

close-up-photo-of-white-and-blue-bird

In May, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Acipenser ruthenus (sterlet)
  • Arvicanthis niloticus (African grass rat)
  • Cannabis sativa (eudicot)
  • Crassostrea gigas (Pacific oyster)
  • Cyclopterus lumpus (lumpfish)
  • Drosophila albomicans (fly)
  • Drosophila guanche (fly)
  • Drosophila innubila (fly)
  • Esox lucius (northern pike)
  • Gymnodraco acuticeps (bony fish)
  • Hippoglossus hippoglossus (Atlantic halibut)
  • Marmota flaviventris (yellow-bellied marmot)
  • Melopsittacus undulatus (budgerigar)
  • Osmia lignaria (orchard mason bee)
  • Pangasianodon hypophthalmus (striped catfish)
  • Pantherophis guttatus (snake)
  • Periophthalmus magnuspinnatus (bony fish)
  • Prunus dulcis (almond)
  • Pseudochaenichthys georgianus (South Georgia icefish)
  • Setaria viridis (monocot)
  • Thalassophryne amazonica (bony fish)
  • Thrips palmi (thrip)
  • Trematomus bernacchii (emerald rockcod)
  • Zea mays (maize)

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

Recent RefSeq annotations: barn owl, monarch butterfly and more

800px-Barn_Owl,_Manchester_area,_UK,_by_Andy_Chilton_2016-07-06_(Unsplash)In February and March, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Amblyraja radiata (thorny skate)
  • Catharus ustulatus (Swainson’s thrush)
  • Chelonoidis abingdonii (Abingdon island giant tortoise)
  • Chiroxiphia lanceolata (lance-tailed manakin)
  • Danaus plexippus plexippus (monarch butterfly)
  • Daphnia magna (crustacean)
  • Drosophila grimshawi (fly)
  • Drosophila mojavensis (fly)
  • Drosophila sechellia (fly)
  • Homo sapiens (human)
  • Hylobates moloch (silvery gibbon)
  • Lontra canadensis (Northern American river otter)
  • Lynx canadensis (Canada lynx)
  • Nasonia vitripennis (jewel wasp)
  • Odontomachus brunneus (ant)
  • Petromyzon marinus (sea lamprey)
  • Phocoena sinus (vaquita)
  • Rattus rattus (black rat)
  • Rhinolophus ferrumequinum (greater horseshoe bat)
  • Strigops habroptila (Kakapo)
  • Taeniopygia guttata (zebra finch)
  • Tyto alba (Barn owl)

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

The next RefSeq FTP release number will skip to 200

NCBI’s Reference Sequence (RefSeq) FTP release numbers will increment to 200 for the next release and skip over the numbers 100-199. The current, March 2020 release, is release 99. The next bi-monthly release in May 2020 will be release 200.  This change is to avoid overlapping with the release numbers of the completely independent RefSeq annotation releases for the eukaryotic genomes we annotate, which are currently in the range 100-109, for example Mus musculus Annotation Release 108. Continue reading “The next RefSeq FTP release number will skip to 200”

Fifteen new NCBI annotations in RefSeq: flies, harbor seal and more

Fifteen new NCBI annotations in RefSeq: flies, harbor seal and more

In January and February, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Aythya fuligula (tufted duck)
  • Camelus ferus (Wild Bactrian camel)
  • Corvus moneduloides (New Caledonian crow)
  • Coturnix japonica (Japanese quail)
  • Drosophila ananassae (fly)
  • Drosophila virilis (fly)
  • Etheostoma spectabile (orangethroat darter)
  • Hylobates moloch (silvery gibbon)
  • Mustela erminea (ermine)
  • Nematostella vectensis (starlet sea anemone)
  • Nomia melanderi (Alkali bee)
  • Phoca vitulina (harbor seal)
  • Sapajus apella (Tufted capuchin)
  • Thamnophis elegans (Western terrestrial garter snake)
  • Xiphophorus hellerii (green swordtail)

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

Important changes to the genomes FTP site in February

We have added the latest NCBI Eukaryotic Genome Annotation Pipeline results for the more than 580 species that we annotate to the genomes/refseq directory on the genomes FTP area. As we announced in December, we will stop publishing annotation results to the genus_species directories (example: genomes/Xenopus_tropicalis) on the genomes FTP site effective February 1, 2020. We will also move existing genus_species directories to genomes/archive/old_refseq during the month of February.X_t_assemblyFigure 1. The Assembly page for the Xenopus tropicalis UCB Xtro 10.0 (GCF_000004195.4) showing the blue download button. Annotation results such as the RefSeq transcript alignments that can be downloaded from the web page are now also under the genomes/refseq directory on the FTP site. The FTP path to the .bam alignment files is in red.

These FTP changes do not affect the Assembly download function. As always, you can download assembly data using the blue Download button on the web pages (Figure 1).

 

December 2019 RefSeq annotations: human, Tasmanian devil and more

tasmanian devil sits, looking to the right

In December, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Anarrhichthys ocellatus (wolf-eel)
  • Apis florea (little honeybee)
  • Contarinia nasturtii (swede midge)
  • Cucumis sativus (cucumber)
  • Galleria mellonella (greater wax moth)
  • Homo sapiens (human)
  • Nasonia vitripennis (jewel wasp)
  • Oncorhynchus kisutch (coho salmon)
  • Oreochromis aureus (blue tilapia)
  • Piliocolobus tephrosceles (Ugandan red Colobus)
  • Sarcophilus harrisii (Tasmanian devil)
  • Xenopus tropicalis (tropical clawed frog)

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

August-October 2019 RefSeq annotations: mouse, firefly and more

mouse with dark brown fur, eating

Recently, the NCBI Eukaryotic Genome Annotation Pipeline has released new annotations in RefSeq for the following organisms:

  • Aedes albopictus (Asian tiger mosquito)
  • Aquila chrysaetos chrysaetos (golden eagle)
  • Archocentrus centrarchus (flier cichlid)
  • Calypte anna (Anna’s hummingbird)
  • Camarhynchus parvulus (bird)
  • Camelus dromedarius (Arabian camel)
  • Cannabis sativa (hemp)
  • Chanos chanos (milkfish)

Continue reading “August-October 2019 RefSeq annotations: mouse, firefly and more”