Tag: Eukaryotic genome annotation
RefSeq release 217 is now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.
As of March 8, 2023, this full release incorporates genomic, transcript, and protein data, containing:
The release is provided in several directories as a complete dataset and divided by logical groupings. Continue reading “RefSeq Release 217”
In December and January, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-nine new annotations in RefSeq for the following organisms:
The RefSeq eukaryotic genome annotation pipeline (EGAP) is moving to a new annotation naming format that can be used to unambiguously reference both the genome assembly and the RefSeq annotation. This will improve clarity when reporting the data you use and make the data more FAIR (Findable, Accessible, Interoperable, and Reusable). The new naming convention applies to all eukaryotic annotations released after December 15, 2022.
Historically, RefSeq EGAP has used an integer to identify a particular annotation release, such as Homo sapiens Annotation Release 110. This method provides no information on the assembly used for the annotation. In the new RefSeq naming system, annotation releases are designated by a combination of the assembly identifier (e.g., GCF_000001405.40) and an annotation name (e.g., RS_2022_04). The annotation name consists of an RS prefix to indicate RefSeq annotation, and the year and month that it was generated, RS_YYYY_MM. You should always use the annotation name in combination with the corresponding assembly accession.version, for example, GCF_026419915.1-RS_2022_12 (as shown in Figure 1). This ensures that you’re always using the name that defines a specific annotation for a specific genome assembly. If you use only part of the name, it will be ambiguous.
Figure 1. The annotation section of the Datasets Genome page for the assembly bHarHar1 for the harpy eagle (Harpia harpyja) showing the new annotation release GCF_026419915.1-RS_2022_12. Continue reading “Announcing New Names for Eukaryotic Genome Annotations in RefSeq!”
Comparative genomics is a science that compares genomic data either within a species or across species to answer questions in biomedicine. Laboratory experiments can then investigate the functional impact of those genomics similarities and differences. The history of comparative genomics goes back to the mid-1990s, but comparative genomics is now accelerating. A flood of new data is emerging as DNA sequencing technology becomes cheaper and commoditized. While this growth poses many challenges to current tools and approaches, it also offers immense opportunity for scientific research and understanding. These insights continue to reveal novel model organisms that can further the impact of comparative genomics on human health. Continue reading “NIH Comparative Genomics Resource project”
In October and November, the NCBI Eukaryotic Genome Annotation Pipeline released thirty-one new annotations in RefSeq for the following organisms:
NCBI is looking forward to seeing you in person at the International Plant and Animal Genome Conference (PAG 30), January 13-18, 2023 in San Diego, California.
We’re especially excited to share our recent efforts on the NIH Comparative Genomics Resource (CGR), a multi-year National Library of Medicine (NLM) project to maximize the impact of eukaryotic research organisms and their genomic data resources on biomedical research.
We also want to hear from you! If you’re interested in sharing your feedback on your needs and experiences involving comparative genomics tools to inform CGR, consider joining our Feedback Session.
RefSeq release 215 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 November 7, 2022, and contains 335,372,031 records, including 244,583,657 proteins and sequences from 125,116 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 215”
In August and September, the NCBI Eukaryotic Genome Annotation Pipeline released thirty-eight new annotations in RefSeq for the following organisms:
RefSeq release 214 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 September 12, 2022, and contains 328,588,569 records, including 239,609,016 proteins, 47,387,931 RNAs, and sequences from 123,394 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.
Foreign contamination screening
Introducing the new Foreign Contamination Screen (FCS) tool! If you produce assembled genomes, check out FCS, a tool you can run yourself to improve your genome assemblies and facilitate high-quality data submissions to GenBank. FCS is part of the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms. See our previous blog post to learn how FCS enhances contaminant detection sensitivity. Continue reading “RefSeq release 214 is available!”
RefSeq release 216 is now available online, from the FTP site, and through NCBI’s new resource, Datasets.
This full release incorporates genomic, transcript, and protein data available as of January 9, 2023, and contains 342,395,932 records, including 249,868,639 proteins, 49,869,497 RNAs, and sequences from 128,299 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 216” →