Tag: Eukaryotic genome annotation

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”

A new service to evaluate the quality of your assembled genome!

A new service to evaluate the quality of your assembled genome!

Are you wondering about the quality of a human, mouse or rat genome that you have assembled?

We offer a new service for evaluating the completeness, correctness, and base accuracy of your human, mouse or rat genome assembly compared to a reference assembly. You simply provide NCBI with one or more assemblies in FASTA format and we will do an annotation-based evaluation of the genome(s) using the expert-curated, high-confidence RefSeq transcripts for the species.

Continue reading “A new service to evaluate the quality of your assembled genome!”

RefSeq release 208 is available!

RefSeq release 208 is available!

RefSeq release 208 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 September 7, 2021, and contains 288,903,207 records, including 210,703,648 proteins, 40,213,945 RNAs, and sequences from 113,002 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq release 208 is available!”

New RefSeq annotations for human, zebra finch, great white shark and more!

New RefSeq annotations for human, zebra finch, great white shark and more!

In May and June, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for 27 organisms.

This release includes new annotations for human, zebra finch, golden eagle, sea urchin, snowfinch, Arctic fox, clawed frog, great white shark, and more:

Continue reading “New RefSeq annotations for human, zebra finch, great white shark and more!”

RefSeq release 207 is available!

RefSeq release 207 is available!

RefSeq release 207 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 July 12, 2021, and contains 285,425,070 records, including 209,035,492 proteins, 39,039,901 RNAs, and sequences from 112,462 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq release 207 is available!”

Announcing RefSeq Release 206!

Announcing RefSeq Release 206!

RefSeq Release 206 is now available. This release includes the following:

Updated human genome Annotation Release 109.20210514
Updated Annotation Release 109.20210514 is an update of NCBI Homo sapiens Annotation Release 109. The annotation report is available here. The annotation products are available in the sequence databases and on the FTP site.

Other new eukaryotic genome annotations
This release includes new annotations generated by NCBI’s eukaryotic genome annotation pipeline for 45 additional species, including: Continue reading “Announcing RefSeq Release 206!”

Vertebrate Genome Project genome assemblies annotated by NCBI

Vertebrate Genome Project genome assemblies annotated by NCBI

NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species.  See the VGP press release  for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank  and the European Nucleotide Archive.  NCBI has annotated 94 of the VGP assemblies from 85 species using the NCBI Eukaryotic Genome Annotation Pipeline.

These sequence and annotation data are available through NCBI web resources including Gene, Assembly, Nucleotide, Protein, and Datasets and are included in the GenBank and RefSeq releases. You can browse the assemblies in the Genome Data Viewer  and  download metadata, sequence, and annotation data for the latest assemblies in the VGP BioProject using the NCBI Datasets command-line tools  as shown below. Continue reading “Vertebrate Genome Project genome assemblies annotated by NCBI”