Tag: CGR

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:

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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. 

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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.

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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.