In July, August, and September, the NCBI Eukaryotic Genome Annotation Pipeline released fifty-six new annotations in RefSeq!
- Achroia grisella (moth)
- Acipenser ruthenus (sterlet)
- Ahaetulla prasina (snake)
- Alligator mississippiensis (American alligator)
- Ammospiza caudacuta (bird)
- Ammospiza nelsoni (bird)
- Anopheles bellator (mosquito)
- Anopheles coustani (mosquito)
- Anopheles ziemanni (mosquito)
- Arachis stenosperma (eudicot)
- Carassius carassius (crucian carp)
- Centropristis striata (black seabass)
- Cornus florida (flowering dogwood) (pictured)
- Corylus avellana (European hazelnut)
- Corythoichthys intestinalis (scribbled pipefish) Continue reading “New Annotations in RefSeq!”
Using the NIH Comparative Genomics Resource (CGR) to gain knowledge about less-researched organisms
The scientific community relies heavily on model organism research to gain knowledge and make discoveries. However, focusing solely on these species misses valuable variation. Comparative genomics allows us to use knowledge from a model species, such as Saccharomyces cerevisiae, to understand traits in other, related organisms, such as Saccharomyces pastorianus or Saccharomyces eubayanus. Applying this information may provide valuable insight for other less-researched organisms. The National Institutes of Health (NIH) Comparative Genomics Resource (CGR) offers a cutting-edge NCBI toolkit of high-quality genomics data and tools to help you do just that. Continue reading “Comparing Yeast Species Used in Beer Brewing and Bread Making”
Using the NIH Comparative Genomics Resource (CGR) to understand susceptibility to SARS-CoV-2 and other infections
Are you conducting research on animal-mediated transmission of human viral infections, such as COVID-19? The National Institutes of Health (NIH) Comparative Genomics Resource (CGR) offers a cutting-edge NCBI toolkit of high-quality genomics data and tools to help with comparative genomics analysis for eukaryotic genes, such as Angiotensin-converting enzyme 2 (ACE2) which is targeted by SARS-CoV-2.
NCBI resources have been beneficial in helping the scientific community understand viral infections associated with public health crises, such as COVID-19 and Influenza, and can be used for study of emerging viruses that may represent new threats. Continue reading “Which animals can catch and transmit human viral infections?”
In April, May, and June, the NCBI Eukaryotic Genome Annotation Pipeline released eighty-two new annotations in RefSeq!
- Homo sapiens (human) T2T-CHM13v2.0 now includes many more alternative splice variants
- Homo sapiens (human) GRCh38.p14 includes all transcripts from MANE v1.2, and includes over 78,000 new RefSeq Functional Element (RefSeqFE) features added since our last annotation in 2022
- Mus musculus (house mouse) GRCm39 integrates curation for over 3,000 genes and 14,000 transcripts since September 2020
- Rattus norvegicus (Norway rat) mRatBN7.2, including curation of over 5000 genes since our last annotation in 2021
New annotations: Continue reading “New Annotations in RefSeq!”
Legacy pages now redirect
Effective July 10, 2023, NCBI’s Assembly and Genome record pages now redirect to new NCBI Datasets pages. As previously announced, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.
The following pages have been updated:
- The NCBI Assembly record pages now redirect to the new NCBI Datasets Genome record pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST.
- The NCBI Genome record pages now redirect to the NCBI Datasets Taxonomy record pages that provide a taxonomy-focused portal to genes, genomes, and additional NCBI resources.
During this transition, you will have the option to return to the legacy Genome and Assembly record pages. We will remove the legacy pages in early 2024. Continue reading “New & Improved NCBI Datasets Genome and Assembly Pages “
Do you need to work with variant data mapped to historical human RefSeq transcript versions? To make it easier to map your data to the current GRCh38 reference genome and MANE transcripts, we’re now providing a collection of RefSeq transcript alignments including both the latest versions in the GCF_000001405.40-RS_2023_03 annotation release, and older transcripts going back to 1999. The data are available for download from the FTP site.
As shown in the example below (Image 1), you can view these alignments in the Genome Data Viewer by loading the remote bam track (GCF_00001405-RS_2023_03_knownrefseqs_aln.bam) from the FTP site. Continue reading “Now Available! Access to Historical Human Transcript Alignments”
Have you ever wondered how your genetic make-up is different from your neighbor’s? The National Human Genome Research Institute (NHGRI)-funded Human Pangenome Research Consortium (HPRC) has built an initial version of a pangenome reference – a collection of new human reference genome sequences representing 47 individuals from across the globe. Pangenome graphs relate the sequences from the different genomes to one another. The pangenome allows researchers to compare these DNA sequences and get a more detailed view of the range of human genetic variation. This is the first step toward the HPRC’s goal of building a pangenome reference comprised of the genomes of 350 individuals from diverse genetic backgrounds. Continue reading “Now Available! Access Data from the Human Pangenome Research Consortium (HPRC) at NCBI”
Unlock the full potential of eukaryotic research organisms and their genomic data with the National Institutes of Health (NIH) Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses through community collaboration as well as an NCBI toolkit of interconnected, interoperable data and tools.
Comparative genomics is a field of study that uses the genomes of many different organisms to help us understand basic biological processes and human disease. NCBI is developing CGR to help researchers take full advantage of the rapidly growing number of eukaryotic organisms that, due to recent technological advances, now have sequenced genomes and associated data that can be used in these types of studies. Its NCBI toolkit offers new and modern resources for such analyses, and its emphasis on community collaboration brings new opportunities to share and connect data. Continue reading “Revolutionize your research with the NIH Comparative Genomics Resource (CGR)”
In February and March, the NCBI Eukaryotic Genome Annotation Pipeline released forty-two new annotations in RefSeq for the organisms listed below. Additionally, interim builds for over sixty species were run during that time period to fix some issues with gene symbol assignment.
As of September 2023, NCBI’s Genome Decoration Page (GDP) will no longer be available. Due to low usage of GDP, we are focusing our development efforts on our more popular resources and tools.
If you are using GDP to view your data mapped to genomes, we encourage you to check out our Genome Data Viewer (GDV) if you haven’t already. You can upload your data for display in GDV and export PDF or SVG images of your view.
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