Venturing beyond the genes: New RefSeq Functional Elements publication!

If you’re curious about genome annotation beyond the genes, then read on! We previously blogged about our RefSeq Functional Elements resource, which provides annotation of experimentally validated, non-genic functional elements in human and mouse. Now, to kick off 2022, we’re delighted to announce a new publication in the January issue of Genome Research:

Farrell CM, Goldfarb T, Rangwala SH, Astashyn A, Ermolaeva OD, Hem V, Katz KS, Kodali VK, Ludwig F, Wallin CL, Pruitt KD, Murphy TD. RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. Genome Res. 2022 Jan;32(1):175-188. doi: 10.1101/gr.275819.121. Epub 2021 Dec 7. PMID: 34876495.

Figure 1. Workflow for production of the RefSeq Functional Elements dataset. Full cylinders represent databases, the half-cylinder represents the indicated data source, and rectangles represent actions. Further details can be found in the publication.

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RefSeq Release 210 is available

RefSeq Release 210 is available

RefSeq Release 210 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 January 3, 2022, and contains 302,482,881 records, including 220,595,192 proteins, 42,453,222 transcripts, and sequences from 115,929 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 210 is available”

PAG XXIX – NCBI Events Have Been Canceled

PAG XXIX – NCBI Events Have Been Canceled

Important COVID-19 Update

Due to the increase in COVID-19 cases across the country, the International Plant and Animal Genome Conference (PAG XXIX) will no longer take place in person on January 8-12, 2022, in San Diego, California.

Although PAG has decided to offer plenary talks and workshop sessions via Zoom to all registered attendees and exhibitors, all NCBI official events have been canceled, including the NCBI Genome Resources workshop and listening session. NCBI posters will be available online and NCBI presenters will continue to support additional workshops that are participating in the virtual event.

Please join our NCBI presenters online at the following talks:

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GenBank Release 247.0

GenBank release 247.0 (12/19/2021) is now available on the NCBI FTP site. This release has 16.47 trillion bases and 2.59 billion records. 

The current release has 234,557,297 traditional records containing 1,053,275,115,030 base pairs of sequence data. There are also 1,734,664,952 WGS records containing 14,922,033,922,302 base pairs of sequence data, 514,158,576 bulk-oriented TSA records containing 455,870,853,358 base pairs of sequence data, and 109,379,021 bulk-oriented TLS records containing 41,143,480,750 base pairs of sequence data. Continue reading “GenBank Release 247.0”

Join NCBI at PAG XXIX

Join NCBI at PAG XXIX

Introducing the NIH Comparative Genomics Resource (CGR)

NCBI is looking forward to seeing you in person at the International Plant and Animal Genome Conference (PAG XXIX), January 8-12, 2022 in San Diego, California. We’re especially excited to introduce our newest endeavor – the NLM initiative known as the NIH Comparative Genomics Resource (CGR)– a platform we are developing to support comparative analyses of sequenced eukaryotic research organisms. Understanding and supporting the needs of researchers is a fundamental element in the development of CGR and is critical to its future success in supporting a large and diverse collection.

Please join NCBI for the following events to learn more about CGR and how you can inform its development:

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NCBI Trace database to be retired in June 2022. Data available in SRA.

NCBI Trace database to be retired in June 2022. Data available in SRA.

The Trace Archive at NCBI will be retired as of June 17, 2022. You may continue to retrieve Trace Archive content by searching the Sequence Read Archive (SRA) using TI number, organism, or center name at the time of retirement.

Continue reading “NCBI Trace database to be retired in June 2022. Data available in SRA.”

Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon Highlights

Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon Highlights

The National Institutes of Health (NIH) Office of Data Science Strategy (ODSS), the National Library of Medicine’s (NLM’s) National Center for Biotechnology and Information (NCBI), and the Department of Energy’s (DOE’s) Office of Biological and Environmental Research (BER) hosted scientists from around the world for a virtual Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon. The codeathon, held September 27-October 1, 2021, attracted experts from national laboratories including the Los Alamos National laboratory, research institutions including the Joint Genome Institute, and students from universities across the world to develop benchmarking approaches to address challenges in conducting large-scale analyses of metagenomic data.

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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!