Tag: Genome annotation

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!

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!

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 coliMycobacterium 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!

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 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”

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.

Continue reading “RefSeq Release 205 is available!”

New release of the Read Assembly and Annotation Pipeline Tool (RAPT), now 2X faster!

There is a new release of the Read assembly and Annotation Pipeline Tool (RAPT) available from our GitHub site. RAPT is a one-step application for the genome assembly and gene annotation of archaeal and bacterial isolates that can run on your local computer or the Google Cloud Platform (GCP). With this new release, jobs will run twice as fast as with the December release. For example, we have assembled and annotated a Salmonella enterica genome in under an hour on a 16-CPU machine with the new release.
We have also added several new features based on your feedback including:

  1. The –stop-on-errors flag that will stop the process if there evidence from the average nucleotide identity check that there is sample mix-up or contamination by other bacteria.
  2. The ability to accept forward and reverse reads of paired-end runs in separate files. These can be compressed (gzip) files.

Finally, thanks to all who came to our webinar in December and provided their comments! For these who couldn’t join us, you can now view the recording on our YouTube channel.

Contact us at prokaryote-tools@ncbi.nlm.nih.gov with any question and to let us know if you would like to become a beta-tester for RAPT.