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.
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!
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.
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!”→
The genomes table (Figure 1) now offers filters for:
Reference genomes — switch it on to only show reference or representative genomes
Annotated — switch it on to only show annotated genomes
Assembly level — use the assembly level slider to select higher-quality genomes
Year released — use the slider to limit your results to recent genomes
In addition, the new Actions column connects you to NCBI’s Genome Data Viewer, BLAST, and Assembly. The Text filter box lets you search by the name of the assembly, species/infraspecies, or submitter.Figure 1. The new Datasets Genomes page with primate assemblies showing the STATUS switches (reference genomes, annotated); expanded filters section with ASSEMBLY LEVEL and YEAR RELEASED sliding selectors; and the Actions column menu with access to Assembly details, BLAST, the Genome Data Viewer, and Download options. Continue reading “Introducing the new NCBI Datasets Genomes page”→
You can now retrieve genome data using the NCBI Datasetscommand-line tool and API by simply providing a BioProject accession. You can go directly from a BioProject accession to genome data even when the BioProject accession is the parent of multiple BioProjects (Figure 1).
If you use Sequin to submit prokaryotic or eukaryotic genome sequences to GenBank, you need to be aware that Sequin will be retired in January 2021. Genome Workbench’s Submission Wizard, which is already available for submitting annotated genomes, will be the submission tool to use for annotated genomes going forward.
Genome Workbench is desktop software that offers a rich set of integrated tools for studying and analyzing genetic data. You can explore and compare data from multiple sources, including the NCBI databases or the your own private data. The Submission Wizard, available since 2019, allows you to prepare submissions of single genomes where all sequences come from the same organism. This interface (Figure 1) is particularly valuable for:
Eukaryotic genomes with annotations, for example those prepared with tbl2asn
Prokaryotic genomes annotated by non-NCBI tools including Prokka and RAST.
Please register to attend our webinar on November 18 to see how to use Genome Workbench to prepare a submission.
(Note: You should continue to submit organelle and viral genomes using BankIt. Please visit the Submission Portal page for information on other submission options.)
Do you need to download a lot of genomic data? Maybe you need all primate reference genomes or maybe you need just a few really big genomes? Prior to the advent of NCBI Datasets, downloading such a large amount of data could be a frustrating and time consuming experience involving failed downloads and writing custom scripts.
NCBI Datasets makes large genome downloads simpler, faster, and more reliable. You don’t have to write a script. You can be sure you get all the data requested. And sharing the data is easier than ever. Figure 1 shows an example data download process using Datasets.
Figure 1. Downloading and processing genomic data using NCBI Datasets. The example shows downloading the set of RefSeq primate assemblies through the Datasets web interface. Since the downloaded files would exceed 15GB, the file comes as a “dehydrated bag” — a small, easily downloaded, zipped file with metadata and links to download the data. You can “rehydrate” the unzipped dehydrated files — fill them with the corresponding data — using the datasets command-line tool.
The Prokaryote type strain report provides information on type-strains for over 18,000 species. We revised and expanded the report to make it easier to identify cases where sequencing or establishing type material would have the biggest impact on improving prokaryote taxonomy and accurate identification. These cases include species with designated type strains but without a sequenced type strain assembly and species without designated type material. We hope that the community will prioritize sequencing type strains for the former set of species (Table 1) and establishing a neotype or reftype, where applicable (as defined in Cuifo et al 2018) for the latter set (Table 2).
Table 1. The top 10 candidate species for sequencing type-strains sorted by the number of assemblies. These have designated type strains but no type strain assembly. We generated the list by sorting by “number of assemblies from type materials per species”, then by decreasing “number of assemblies per taxon”, then filtering out “type materials and coidentical strains” = “na”.
Table 2. The top 10 candidates for proposing a reftype assembly, or neotype where applicable sorted by the number of assemblies. These species have no designated type strain. We generated the list by selecting for “type materials and coidentical strains” = “na”, “number of assemblies from type materials per species” = 0, and sorting by decreasing “number of assemblies per taxon”, then filtering out Candidatus.
As we described in an earlier post, GenBank uses average nucleotide identity (ANI) analysis to find and correct misidentified prokaryotic genome assemblies. You can now access ANI data for the more than 600,000 GenBank bacterial and archaeal genome assemblies through a downloadable report (ANI_report_prokaryotes.txt) available from the genomes/ASSEMBLY_REPORTS area of the FTP site. The README describes the contents of the report in detail. You can use the ANI data to evaluate the taxonomic identity of genome assemblies of interest for yourself.
The new ANI_report_prokaryotes.txt replaces the older ANI_report_bacteria.txt in the same directory. We are no longer updating the ANI_report_bacteria.txt file and will remove it after 31st May 2020.