Tag: Genome annotation

Come see NCBI at the ASM Microbe Conference 2022

The American Society of Microbiology (ASM) Microbe conference is back, and scheduled to take place in-person, June 9th-13th in Washington, D.C.

NCBI staff member Dr. Michael Feldgarden will be recognized by ASM with an award for his research. Other NCBI staff will present posters on NCBI resources and will also be available at our booth (#1128) to address your questions. Drop by to see what’s new and provide your feedback. We hope to see you there! Check out NCBI’s schedule of activities: Continue reading “Come see NCBI at the ASM Microbe Conference 2022” →

Announcing Human Annotation Release 110

The annotation of human assemblies GRCh38.p14 and T2T-CHM13v2.0

We are happy to announce the first de novo annotation of human T2T-CHM13v2.0, the gap-less assembly generated by the T2T Consortium, and the full re-annotation of the human reference assembly, GRCh38.p14. We hope the results will serve both the needs of those eager to explore newly sequenced regions of the genome, including telomeres and centromeres, and those interested in refreshing their interpretation of the human reference, in light of recently curated transcripts and new transcriptomic and other data incorporated in the annotation. Continue reading “Announcing Human Annotation Release 110” →

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.

Continue reading “Venturing beyond the genes: New RefSeq Functional Elements publication!” →

Bulk Sequence-Cytogenetic Conversion Service to be retired in April 2022

The Bulk Sequence-Cytogenetic Conversion Service tool at NCBI will be retired in April 2022. This tool obtained cytogenetic locations for a list of annotated genes, SNPs, or assembly coordinates from human, fruit fly, mouse, or rat genomes. It also obtained sequence coordinates for cytogenetic locations for these genomes. This web service will be retired due to low usage and obsolescence.

The underlying cgi (bp2band) will be retained and continues to drive the Ideogram service within the Genome Data Viewer (GDV) and the Genome Decoration Page. Researchers interested in understanding where features are located relative to chromosome cytogenetic banding should check out the Genome Decoration Page, where you can enter a file of genome annotations and display them on a ideogram of your assembly of interest. You can also go directly to a cytogenetic location on a genome using the search box in the GDV genome browser.

Feel free to contact us with any questions or concerns at info@ncbi.nlm.nih.gov.

Announcing the RefSeq annotation of sheep ARS-UI_Ramb_v2.0!

The new reference assembly for sheep is now annotated! Assembly ARS-UI_Ramb_v2.0 is made of 142 scaffolds, a drop from 2,640 in the 2017 assembly Oar_rambouillet_v1.0. With a contig N50 of 43 Mb, ARS-UI_Ramb_v2.0 is 15 times more contiguous than the first assembly of the Rambouillet breed.

Annotation Release 104 (AR 104) of ARS-UI_Ramb_v2.0 reflects these improvements. Nearly 200 more coding genes have a 1:1 ortholog in the human genome than in the annotation of Oar_rambouillet_v1.0 (AR 103). The number of coding models annotated as partial is down 35% from 165 to 107, and the number of coding models labeled low quality due to suspected indels or base substitutions in the underlying genomic sequence decreased by 51% (1646 to 796). Based on BUSCO analysis, 99.1% of the models (cetartiodactyla_odb10) are complete in AR 104 versus 98.8% in AR 103. Details of this annotation, including statistics on the annotation products, the input data used in the pipeline and intermediate alignment results, can be found here. Continue reading “Announcing the RefSeq annotation of sheep ARS-UI_Ramb_v2.0!” →

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!” →

Announcing the re-annotation of RefSeq genome assemblies for E. coli and four other species!

We have re-annotated all RefSeq genomes for Escherichia coli, Mycobacterium tuberculosis, Bacillus subtilis, Acinetobacter pittii, and Campylobacter jejuni using the most recent release of PGAP. You will find that more genes now have gene symbols (e.g. recA). Your feedback indicated that the lack of symbols was an impediment to comparative analysis, so we hope that this improvement will help.

The number of re-annotated genomes is 25,619 for E. coli, 470 for B. subtilis, 6,828 for M. tuberculosis, 316 for A. pittii, and 1,829 for C. jejuni. On average, the increase in gene symbols is 30% in E. coli, 110% in B. subtilis, 57% in M. tuberculosis, 94% in A. pittii and 62% in C. jejuni (see Figure 1). After re-annotation, on average, 73% of PGAP-annotated E. coli genes and 79% of B. subtilis have symbols (35% for M. tuberculosis, 40% for A. pittii and 46% for C. jejuni). We assigned symbols to the annotated genes by calculating the orthologs between the genome of interest and the reference assembly for the species, and transferring the symbols from the reference genes to their orthologs in the annotated genomes.

Figure 1: Average and standard deviation of the number of genes annotated with symbols per genome, in the previous (blue) and the current annotation (orange).

Continue reading “Announcing the re-annotation of RefSeq genome assemblies for E. coli and four other species!” →

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!” →

New RefSeq annotations for Siamese fighting fish, common toad, swan, platypus and more!

In March and April, the NCBI Eukaryotic Genome Annotation Pipeline released thirty-two new annotations in RefSeq for the following organisms: Continue reading “New RefSeq annotations for Siamese fighting fish, common toad, swan, platypus and more!” →

New NCBI Datasets home and documentation pages provide easier access

NCBI Datasets, the new set of services for downloading genome assembly and annotation data (previous Datasets posts), has redesigned and reorganized web pages to make it easier to find and access the services and documentation you need.

NCBI Datasets has a fresh new homepage (Figure 1) highlighting the types of data available through our tools. Available data include genome assemblies, genes, and SARS-CoV-2 genomic and protein data. You can easily access these from the new page or learn more with our new documentation pages.

Figure 1. Features of the new Datasets homepage with quick access to help documentation including the Quickstart and How-to guides as well as access to Genome, Gene, and Coronavirus Data, and the Datasets and Dataformat command-line tools. Continue reading “New NCBI Datasets home and documentation pages provide easier access” →