Tag: RefSeq

March & April annotations in RefSeq: chimpanzee, human & more

Chimpanzees_in_Uganda_(5984913059)The NCBI Eukaryotic Genome Annotation Pipeline has recently released new annotations in RefSeq for the following organisms:

  • Bombus impatiens (common eastern bumble bee)
  • Brachypodium distachyon (stiff brome)
  • Cimex lectularius (bed bug)
  • Desmodus rotundus (common vampire bat)
  • Halyomorpha halys (brown marmorated stink bug)
  • Homo sapiens (human, more information can be found here)
  • Lingula anatina (brachiopod)
  • Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise)
  • Oncorhynchus tshawytscha (Chinook salmon)
  • Oryzias melastigma (Indian medaka)
  • Pan troglodytes (chimpanzee)
  • Physcomitrella patens (moss)
  • Populus trichocarpa (black cottonwood)
  • Rosa chinensis (China rose)
  • Selaginella moellendorffii (club-moss)
  • Terrapene mexicana triunguis (Three-toed box turtle)

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

Human annotation release 109 for GRCh38.p12 is available in RefSeq

Human annotation release 109 for GRCh38.p12 is available in RefSeq

You can now download human annotation release 109 on FTP or explore it in the Genome Data Viewer, in the Gene database, and with BLAST.

Highlights in release 109:

  • A total of 20,203 protein-coding genes and 17,871 non-coding genes were annotated.
  • The number of annotated curated transcripts increased by 17% and genes with two or more curated alternative variants increased by 8%.
  • The annotation includes 6,862 features and 2,075 GeneIDs for non-genic functional elements, such as regulatory regions and known structural elements. For example, see the opsin locus control region (OPSIN-LCR).

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RefSeq release 87 available

RefSeq release 87 available

RefSeq release 87 is now accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript and protein data available as of March 5, 2018 and contains 155,118,991 records, including 106,245,682 proteins, 21,923,574 RNAs, and sequences from 77,225 organisms. The release is provided in several directories as a complete dataset and as divided by logical groupings.

Starting in July 2018, SNP variation features will no longer be in RefSeq genome assembly records – chromosome and contig records with NC_, NT_, NW_ and AC_ accession prefixes.  The RefSeq release notes have more information about this change.

RefSeq release 86 is now public

RefSeq release 86 is now public

RefSeq release 86 is now accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript, and protein data available, as of January 8, 2018 and contains 149,493,466 records, including 102,133,844 proteins, 21,370,778 RNAs, and sequences from 75,218 organisms. The release is provided in several directories as a complete dataset and as divided by logical groupings.

Two important notes follow; please see the RefSeq release notes for more information.

Non-human SNP data dropped

Non-human SNPs were dropped from all RefSeq FTP files in the daily FTP files starting in December 2017, and in this full release (January 2018).

HPRD features removed

We have dropped a set of features, originally imported from HPRD, from human transcript and protein RefSeq records.

5 NCBI articles in 2018 Nucleic Acids Research database issue

5 NCBI articles in 2018 Nucleic Acids Research database issue

The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

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Seventeen new NCBI annotations in RefSeq for cat, maize, clownfish, and more

Seventeen new NCBI annotations in RefSeq for cat, maize, clownfish, and more

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

  • Amphiprion ocellaris (clown anemonefish)
  • Centruroides sculpturatus (bark scorpion)
  • Ceratitis capitata (Mediterranean fruit fly)
  • Cucurbita maxima (winter squash)
  • Cucurbita moschata (crookneck pumpkin)
  • Drosophila hydei (fly)
  • Drosophila willistoni (fly)
  • Felis catus (domestic cat)
  • Leptinotarsa decemlineata (Colorado potato beetle)
  • Maylandia zebra (zebra mbuna)
  • Olea europaea sylvestris (wild olive)
  • Onthophagus taurus (beetle)
  • Piliocolobus tephrosceles (Ugandan red Colobus)
  • Seriola lalandi dorsalis (yellowtail amberjack)
  • Spodoptera litura (moth)
  • Xiphophorus maculatus (southern platyfish)
  • Zea mays (maize)

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

RefSeq release 85 is now public

RefSeq release 85 is now public

RefSeq release 85 is now accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript, and protein data available, as of November 6, 2017, and contains 146,710,309 records, including 100,043,962 proteins, 20,905,608 RNAs, and sequences from 73,996 organisms. The release is provided in several directories as a complete dataset and as divided by logical groupings. See the RefSeq release notes for more information.

Continue reading “RefSeq release 85 is now public” →