We are looking forward to the Biology of Genomes meeting, which will focus on “DNA sequence variation and its role in molecular evolution, population genetics and complex diseases, comparative genomics, large-scale studies of gene and protein expression, and genomic approaches to ecological systems.”
The NIH Comparative Genomics Resource: Amplifying the biology of genomes presented by Valerie Schneider, PhD
On behalf of NIH, NLM is developing the NIH Comparative Genomics Resource (CGR) at NCBI to facilitate organism-spanning data connections and promote new research discoveries. This initiative aims to connect NCBI genomics-associated data types and tools with resources external to NCBI to provide a foundation for reliable comparative analysis for all eukaryotic research organisms. Continue reading “NCBI Posters at the Biology of Genomes Meeting”→
Reduced redundancy. Faster searches. More diverse proteins and organisms in your BLAST results. Check out our new ClusteredNR database – derived from the default BLAST protein nr database by clustering sequences at 90% identity / 90% length (details below). Get quicker results and access to information about the distribution of your hits across a wider range of organisms and evolutionary distances.
You can choose the ClusteredNR database in the Choose Search Set section of the BLAST submission form where you normally pick the BLAST database. Simply select the Experimental databases radio button. You can also select the checkbox to search both ClusteredNR and the standard nr at the same time allowing you to compare results (Figure 1).
NCBI Gene now has descriptive information about genes from the Alliance of Genome Resources for organisms including Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, and Saccharomyces cerevisiae.
Figure 1. The gene summary section of the Drosophila melanogaster slmb Gene Full Report showing the link to the corresponding record at the Alliance of Genome Resources.
The Summary section of the Gene Full Report page has Links to gene pages at the Alliance of Genome Resources (Figure 1). These are also in the right-hand sidebar of the Links to other resources section. In the case of genes that don’t have a RefSeq summary, we use the textual gene descriptions from the Alliance of Genome resources.
The Drosphilaslmb gene record shows the enhancements provided by the Alliance of Genome Resources. The gene_info.gz files on the Gene FTP site also include AllianceGenome references in the dbXrefs column.
Introducing the NIH Comparative Genomics Resource (CGR)
NCBI is looking forward to seeing you in person at the International Plant and Animal Genome Conference (PAG XXIX), January 8-12, 2022 in San Diego, California. We’re especially excited to introduce our newest endeavor – the NLM initiative known as the NIH Comparative Genomics Resource (CGR)– a platform we are developing to support comparative analyses of sequenced eukaryotic research organisms. Understanding and supporting the needs of researchers is a fundamental element in the development of CGR and is critical to its future success in supporting a large and diverse collection.
Please join NCBI for the following events to learn more about CGR and how you can inform its development:
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!
NCBI’s Genome Data Viewer (GDV) now supports visualization and analysis of nearly 400 submitter-annotated chromosome-level assemblies from the INSDC (GenBank/ENA/DDBJ). These submitter-annotated assemblies join more than 1,200 NCBI RefSeq-annotated assemblies available in GDV for hundreds of eukaryotes, spanning fungi, plants, fish, insects, and all major model organisms.
Figure 1. Submitter-annotated Malus domestica (apple) assembly displayed in GDV. GDV provides submitter-provided gene annotation, as well as some additional tracks including interspersed repeats identified by RepeatMasker and six-frame translations (not shown). Red boxes indicate useful tools and panels including a search box, an exon navigator, and interfaces to add user data and conduct NCBI BLAST searches.
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 National Center for Biotechnology Information (NCBI) has several speakers at the upcoming Biodiversity Genomics Conference from September 27 to October 1, 2021.
Valerie Schneider, head of NCBI’s SeqPlus Program and Deputy Director for Sequence Offerings, will present a poster discussing how NCBI’s new comparative genome research focus will enable researchers to explore all eukaryotic research organisms, find related organisms and support additional organism-specific resources that a specific community may have or wish to develop.
Nuala O’Leary, Product Owner, NCBI Datasets will present the latest developments for Datasets, a beta resource that supports intuitive and flexible access to genome data for a broad range of taxa via a redesigned website and command-line tools.
Adelaide Rhodes, Cloud Subject Matter Expert in Education, will present two case studies that emphasize the ease of navigating the new Datasets website as well as the use of command line tools to speed up data discovery for genes and genomes of interest.
Terence Murphy, Product Owner, NCBI RefSeq will present a new tool for genome providers to identify contamination in newly assembled sequences with high sensitivity, specificity, and performance.
The Biodiversity Genomics Conference brings together a global audience to celebrate achievements in genome sequencing across the eukaryotic tree of life, explore current challenges and solutions, and to develop strategies for sequencing and data sharing in the upcoming decade of biodiversity genomics. NCBI has several programs that support the needs of this scientific research group.