Tag: Eukaryotic genome annotation

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”

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI staff will be presenting virtual posters at the Cold Spring Harbor Laboratory  Biology of Genomes Meeting, May 11 -14, 2021. The posters will cover the following topics: 1) a cloud-ready suite of tools (PGAP, RAPT , and SKESA) for assembling and annotating prokaryotic genomes,  2) Datasets — a new set of services for downloading genome assemblies and annotations, and 3) updates on NCBI RefSeq eukaryotic genome annotation, and the Genome Data Viewer (GDV). Read more below for the full abstracts.

The virtual poster gallery opens Tuesday, May 11 at 9:00 a.m. with dedicated time for poster viewing and discussion at 1:00 to 2:00 p.m. through Slack each day. The poster gallery will be open for entire the conference and remain available for six weeks afterwards.  Continue reading “NCBI at CSHL Biology of Genomes, May 11 – 14, 2021”

January-February 2021 RefSeq annotations include dog, fly, rat

Figure 1. This is Tasha, the female boxer used for one of the assemblies annotated for dog (GCF_000002285.5). Image courtesy of the National Human Genome Research Institute.

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

  • Benincasa hispida (wax gourd)
  • Canis lupus familiaris (dog)
  • Corvus cornix cornix (hooded crow)
  • Crotalus tigris (tiger rattlesnake)
  • Culex pipiens pallens (northern house mosquito)
  • Dioscorea cayenensis subsp. rotundata (Guinea yam)
  • Drosophila santomea (fly)
  • Drosophila simulans (fly)
  • Drosophila yakuba (fly)
  • Eucalyptus grandis (rose gum)
  • Hibiscus syriacus (Rose-of-Sharon)
  • Hyaena hyaena (striped hyena)
  • Maniola hyperantus (ringlet)
  • Mauremys reevesii (Reeves’s turtle)
  • Nilaparvata lugens (brown planthopper)

Continue reading “January-February 2021 RefSeq annotations include dog, fly, rat”

Improvements to NCBI Assembly

NCBI’s genome Assembly has a number of significant improvements!

Assembly records now have a link to Primer-BLAST making it easy to design primers in the context of a specific eukaryote genome assembly.  Figure 1 shows the Assembly page for the Genome Reference Consortium Mouse Build 39 (GRCm39) with the link to Primer-BLAST.

Figure 1. The Assembly page for the mouse reference genome (GCF_000001635.27). Showing the new Run Primer-BLAST link, which loads the assembly as a database in the Primer-BLAST search (bottom) and the new expandable note sections, Genome-Annotation-Data in this case. 
Continue reading “Improvements to NCBI Assembly”

View intron feature evidence in the Genome Data Viewer and Sequence Viewer

Are you a researcher who works on gene biology and are interested in alternative splice patterns in your gene or genes of interest?  If so, be sure to explore the intron feature evidence available in graphics views of genome assemblies annotated by NCBI. You can view the NCBI evidence used for calling splice variant for genes, add other intron feature evidence tracks, and use new display and filter options that make it easier to interpret the data .

Figure 1. Graphical view of the monoamine oxidase gene (MAOA, MOAB) region on the human X  chromosome showing intron features tracks (‘RNA-seq intron features, aggregate’ and ‘Intropolis RNA-Seq intron features’). Mousing-over an intron feature activates a tooltip that shows details such as the number of reads with the splice site, the location on the chromosome, the length of the intron and the donor and acceptor bases at the splice site. The Intropolis track was added through the search feature of the Configure Tracks menu and configured (bottom menu) so that the features were sorted by strand and filtered so that only features with greater than 500 reads appear.

Continue reading “View intron feature evidence in the Genome Data Viewer and Sequence Viewer”

October-December eukaryotic genome annotations in Refseq

October-December eukaryotic genome annotations in Refseq

Since October, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for a large number of organisms. We’ve separated them by group; click on “details” to see the full list for each.

Mammals

Pedestrians on pedestrian crosswalk. Top view.

  • Artibeus jamaicensis (Jamaican fruit-eating bat)
  • Arvicola amphibius (Eurasian water vole)
  • Balaenoptera musculus (Blue whale)
  • Cebus imitator (Panamanian white-faced capuchin)
  • Chlorocebus sabaeus (green monkey)
  • Homo sapiens (human)
  • Manis javanica (Malayan pangolin)
  • Manis pentadactyla (Chinese pangolin)
  • Ochotona princeps (American pika)
  • Peromyscus leucopus (white-footed mouse)
  • Pipistrellus kuhlii (Kuhl’s pipistrelle)
  • Sturnira hondurensis (bat)
  • Talpa occidentalis (Iberian mole)
  • Trichosurus vulpecula (common brushtail)

Continue reading “October-December eukaryotic genome annotations in Refseq”