14 new NCBI RefSeq genome annotations are available

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

  • Spinacia oleracea (spinach)
  • Carica papaya (papaya)
  • Zootermopsis nevadensis (termites)
  • Acanthochromis polyacanthus (spiny chromis)
  • Folsomia candida (springtails)
  • Helianthus annuus (common sunflower)
  • Acanthaster planci (crown-of-thorns starfish)
  • Myzus persicae (green peach aphid)
  • Momordica charantia (bitter melon)
  • Pieris rapae (cabbage white)
  • Nilaparvata lugens (brown planthopper)
  • Drosophila obscura (a fly)
  • Canis lupus familiaris (dog)
  • Limulus polyphemus (Atlantic horseshoe crab)

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

RefSeq release 84 available

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RefSeq release 84 is now accessible online, via FTP and through NCBI’s programming utilities.

This full release incorporates genomic, transcript, and protein data available, as of September 11, 2017, and contains 140,627,690 records, including 95,563,598 proteins, 20,356,598 RNAs, and sequences from 72,965 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.

Phasing out support for non-human organisms

As of September 1, 2017, the dbSNP and dbVar databases have stopped accepting submissions for non-human organisms. Submissions for non-human variation will now be accepted by the European Variation Archive, one of our partners in the International Nucleotide Sequence Database (INSDC).

NCBI releases newly designed dbSNP RefSNP Report – Alpha version

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NCBI dbSNP is pleased to announce a newly designed Reference SNP (RefSNP, rs) Report webpage to provide enhanced performance and presentation for access to individual RefSNP records. This Alpha version of the report enables browsing of submitted and computed RefSNP variant data from the redesigned dbSNP build system.

The new RefSNP report (alpha version). You can see all of the sections described in the blog post, like the summary section and the sidebar menu.

Figure 1. The dbSNP RefSNP Report Alpha for rs268.

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Essentials of Glycobiology, Third Edition & New Glycan Website Now Available at NCBI

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Glycobiology—the study of the structure, biosynthesis, biology, and evolution of glycans (the sugar chains synthesized by all living cells)—is a rapidly growing field in the natural sciences, with broad relevance to many areas of basic research, biomedicine, and biotechnology.

NCBI has two new glycobiology resources: the third edition of a definitive work in the field, Essentials of Glycobiology, and a new NCBI Glycans website that includes links to some useful external resources as well as the Symbol Nomenclature for Glycans (SNFG).

essentials of glycobiology

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September 6 NCBI Minute: The NCBI Application Programming Interfaces (APIs)

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On September 6, 2017, we will present a webinar on Application Programming Interfaces (APIs) at NCBI.

Whether you’re new to APIs or are already using them, this webinar has something for you. We’ll introduce you to APIs and what they can be used for, then focus on the diverse group of APIs available to access NCBI databases and tools.

Date and time: Wed, Sep 6, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel.

You can learn about future webinars on the Webinars and Courses page.

GenBank release 221.0 is available via FTP, Entrez and BLAST

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GenBank release 221.0 (8/13/2017) has 203,180,606 traditional records containing 240,343,378,258 base pairs of sequence data. In addition, there are 499,965,722 WGS records containing 2,242,294,609,510 base pairs of sequence data, 186,777,106 TSA records containing 167,045,663,417 base pairs of sequence data, and 1,628,475 TLS records containing 824,191,338 base pairs of sequence data.

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Yellow fever mosquito, 6 other organisms in July RefSeq genome annotations

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

  • Papio anubis (olive baboon)
  • Prunus avium (sweet cherry)
  • Aedes aegypti (yellow fever mosquito)
  • Chenopodium quinoa (quinoa)
  • Hevea brasiliensis (a eudicot)
  • Manihot esculenta (cassava)
  • Carlito syrichta (Philippine tarsier)
Portrait of olive baboon

Papio anubis (olive or anubis baboon)
Source: United States Fish and Wildlife Service: Digital Library System

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

August 30 NCBI Minute: NCBI Hackathons, a framework for rapid prototyping of pipelines for bioinformatics, biomedical informatics and genomics

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NCBI regularly organizes hackathons throughout the United States, where participants work in teams to apply their data science experience with public datasets. In this NCBI Minute, you will hear highlights from recent hackathons, see examples of the software created in these events, and learn how you can participate in future hackathons.

Date and time: Wednesday, August 30, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

September 2017: NCBI to present EDirect workshop at NLM

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On September 18, 2017, NCBI staff will offer a workshop on EDirect, NCBI’s suite of programs for easy command line access to literature and biomolecular records. To join the workshop, please register.

NOTE: This is an in-person workshop at the National Library of Medicine on the NIH campus in Bethesda, MD, USA. The course is limited to 22 participants.

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