Tag: CGR

NCBI Posters at the Biology of Genomes Meeting

NCBI Posters at the Biology of Genomes Meeting

May 10-14, 2022

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.”

NCBI will present three posters to highlight our Comparative Genomics Resource (CGR) and the Allele Frequency Aggregator (ALFA):

  1. 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”

New ClusteredNR database: faster searches and more informative BLAST results

New ClusteredNR database: faster searches and more informative BLAST results

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.

Searching ClusteredNR

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).

Figure 1. The ‘Choose Search Set’ section of the BLAST submission form. Selecting the Experimental databases radio button chooses ClusteredNR. You can also perform simultaneous searches against the clustered and the standard nr by checking ‘Select to compare standard and experimental database.’ Continue reading “New ClusteredNR database: faster searches and more informative BLAST results”

New Gene Information from the Alliance of Genome Resources

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 Drosphila slmb 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.

Join NCBI at PAG XXIX

Join NCBI at PAG XXIX

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:

Continue reading “Join NCBI at PAG XXIX”

Save the Date: NCBI at Plant and Animal Genome (PAGXXIX), Jan 2022

Save the Date: NCBI at Plant and Animal Genome (PAGXXIX), Jan 2022

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 now displays both NCBI RefSeq and submitted assemblies

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 shows a GenBank apple assembly (GCA_004115385) displayed in GDV.

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. 

Continue reading “NCBI’s Genome Data viewer now displays both NCBI RefSeq and submitted assemblies”

A new service to evaluate the quality of your assembled genome!

A new service to evaluate the quality of your assembled genome!

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.

Continue reading “A new service to evaluate the quality of your assembled genome!”

NCBI Presentations at Biodiversity Genomics 2021 Highlight Growing Support for Comparative Genomics

NCBI Presentations at Biodiversity Genomics 2021 Highlight Growing Support for Comparative Genomics

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.