Tag: Human genome

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”

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.

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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!”

RefSeq Release 205 is available!

RefSeq Release 205 is available!

RefSeq release 205 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 March 1, 2021, and contains 269,975,565 records, including 197,232,209 proteins, 36,514,168 RNAs, and sequences from 108,257  organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

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RefSeq release 204 is now available

RefSeq release 204 is now available

RefSeq release 204 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 4, 2021, and contains 262,714,372 records, including 191,411,721 proteins, 35,353,412 RNAs, and sequences from 106,581 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

Updated human genome Annotation Release 109.20201120
Updated Annotation Release 109.20201120 is an update of NCBI Homo sapiens Annotation Release 109.

The annotation report for 109.20201120 is available here. The annotation products are available in the sequence databases and on the FTP site. Continue reading “RefSeq release 204 is now available”

December 2019 RefSeq annotations: human, Tasmanian devil and more

tasmanian devil sits, looking to the right

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

  • Anarrhichthys ocellatus (wolf-eel)
  • Apis florea (little honeybee)
  • Contarinia nasturtii (swede midge)
  • Cucumis sativus (cucumber)
  • Galleria mellonella (greater wax moth)
  • Homo sapiens (human)
  • Nasonia vitripennis (jewel wasp)
  • Oncorhynchus kisutch (coho salmon)
  • Oreochromis aureus (blue tilapia)
  • Piliocolobus tephrosceles (Ugandan red Colobus)
  • Sarcophilus harrisii (Tasmanian devil)
  • Xenopus tropicalis (tropical clawed frog)

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

New human genome annotation release with MANE Select and other improvements!

New human genome annotation release with MANE Select and other improvements!

There’s a new RefSeq annotation available for the human genome, and it’s quite an update!

About the release

Annotation release 109.20190607 is the first release of our new bimonthly annotation schedule as announced in a previous post.   The annotated sequences are  the latest sequences for the GRCh38, patch 13 assembly, GRCh38.p13 (GCF_000001405.39). The chromosome backbone sequences remain the  same, but we’ve added 45 patch sequences representing novel and improved sequences that the Genome Reference Consortium will incorporate into the primary assembly in the future. The new annotation places the latest curated RefSeq transcripts and functional elements on the genome but keeps the same model dataset as in annotation release 109 except when the models have been replaced by curated RefSeqs or other review. We are also flagging MANE and other RefSeq Select transcripts.  Continue reading for more details on these improvements below. You can download the updated annotation here!

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Human genome annotation will be updated every 2 months

NCBI will be updating the human genome RefSeq annotation more frequently to incorporate improvements made to genes and transcripts by RefSeq curation experts. Faster updates will allow us to include the latest datasets.

In the past, we’ve produced a full re-annotation of the human genome about once a year. The last full annotation, Homo sapiens Annotation Release 109, was in March 2018. A full annotation is produced by two main processes:

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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).

Continue reading “Human annotation release 109 for GRCh38.p12 is available in RefSeq”