We will present a variety of talks and posters featuring our clinical and human genetic resources, as well as genome products and tools. We are excited to introduce 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 to biomedical research. If you’re interested in providing feedback that will be used to help drive CGR forward, consider joining our round table discussion.
Check out NCBI’s schedule of activities and events:
In October 2022, NCBI Datasets will release version 14 of our datasets and dataformat command-line tools. This release will contain breaking changes to the command syntax, content of the data packages and data reports. Thank you for your feedback that inspired these new features. We hope they will improve your experience!
We will continue to support CLI v13.x, although new features and improvements will be exclusive to CLI v14.0.0 release and up.
NCBI Datasets supports the NIH Comparative Genomics Resource (CGR), an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms. Join our mailing list to keep up to date with NCBI Datasets and other CGR news.
A new version of the Conserved Domain Database (CDD) is now available. Version 3.20 contains 1,614 new or updated NCBI/CDD-curated domains and now mirrors Pfam version 34 as well as new models from the NCBIfam collection. Fine-grained classifications of the [(+)ssRNA] virus RNA-dependent RNA polymerase catalytic domain, RING-finger/U-box, dimerization/docking domains of the cAMP-dependent protein kinase regulatory subunit, and Galactose/rhamnose-binding lectin domain superfamily have been added, along with many other new models.
We have significantly increased the fraction of CD-Search and interactive BATCH CD-Search queries that yield results showing conserved domain architecture information and attributes that further characterize protein function through links to information-rich resources such as Enzyme Commission (EC) numbers , Gene Ontology (GO) terms, PubMed IDs, and identifiers from the CaZY, TCDB, and MEROPS databases. See our earlier post for additional details. You can access CDD and find updated content on the CDD FTP site at CDD version 3.20.
CD Search 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.
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!”→
Learn about the NIH Comparative Genomics Resource (CGR) Project
The Biodiversity Genomics conference will take place virtually, October 2-7, 2022. This event is hosted by the Earth BioGenome Project and is open and free for all to attend.
NCBI staff will present a variety of recorded talks and posters highlighting various elements of the NIH Comparative Genomics Resource (CGR), including NCBI Datasets and the Comparative Genome Viewer (CGV). CGR is a multi-year National Library of Medicine (NLM) project to maximize the impact of eukaryotic research organisms and their genomic data resources to biomedical research. NCBI is charged with leading CGR development and engaging genomics communities. The CGR project will facilitate reliable comparative genomics analyses for all eukaryotic organisms in collaboration with the genomics community.
Conserved Domain Search (CD Search) results now show domain architecture information and other annotations that further characterize predicted domain and protein function. These include links to PubMed, Gene Ontology (GO) terms, Enzyme Commission (EC) numbers, and the SPARCLE Domain Architecture Viewer. You can use these links on the results to find literature (PubMed), assign biological roles and protein function (GO and EC), and find proteins with the same domain architecture (Domain Architecture Viewer). These annotations are currently available for a limited number of architectures, but we will continue to add them as part of our curation effort.
We are excited to introduce a Foreign Contamination Screen (FCS) tool that you can now run yourself, with enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to GenBank. If you submit genome assembly data to GenBank, the FCS tool is for you!
What is the FCS tool?
FCS, a quality assurance process used to make data suitable for submission, consists of two parts: FCS-adaptor and FCS-GX. FCS-adaptor searches for short sequences that are used as part of the lab preparation process and sometimes wind up in the final assembly by mistake. FCS-GX searches for sequences from a wide range of organisms including bacteria, fungi, protists, viruses, and others to identify sequences that don’t look like they are from the intended organism. In each case, you receive a report of the coordinates and identities of potential contaminants to be reviewed and removed (see Figure 1 for a sample report of the FCS-GX summary output). Both tools are designed to screen both eukaryote and prokaryote genomes.
Figure 1. FCS-GX report showing the summary of contamination identified in a tomato genome. The output indicates there are 83 sequences, adding up to 381 kb total length, to be removed from a mix of insect, fungal, and bacterial sources.
How do I use FCS?
FCS is available from GitHub. Simply download the two programs (FCS-adaptor and FCS-GX), and follow a few steps as outlined in the Quickstart. Both tools are also easy and inexpensive to run on commercial clouds such as Amazon Web Services (AWS) or Google Cloud Platform (GCP), and can screen genomes in a fraction of the time of other approaches.
Why is FCS important?
Having high quality data available for analysis is necessary in order to arrive at accurate conclusions during research. With FCS, rapiddetection of contaminants from foreign organisms in assembled genomes ensures that high value data is being provided for submission and available for reuse. We’ve already used FCS-GX to remove over one hundred megabases of contaminants and thousands of erroneous genes and proteins from previously submitted eukaryote genomes to make the data more useful for all.
We want to hear from you!
We will update the FCS tool based on your feedback, so try it out and let us know what you think. Please contact us with comments and suggestions.
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.
As we previously announced, we are offering a ClusteredNR protein database on the web BLAST service that provides faster searches, greater taxonomic reach, and easier to interpret results than the traditional nr database. We’ve added some new features to the results that make the ClusteredNR even more useful by allowing analyses within each cluster including the ability to:
Align the query to the members of the cluster.
Display Tree View and MSA View the cluster alignment.
Submit the cluster to COBALT to generate a true multiple sequence alignment of the members.
Display a BLAST Taxonomy Report to see the taxonomic distribution of the sources of the members.
Figure 1 shows you how access these in-cluster analysis options. The new Cluster Taxonomy report is shown in Figure 2. Try ClusteredNR yourself — follow this link to set up a search!
We are excited to introduce new and useful updates to the Datasets genome table that let you quickly find and download a genome dataset including genome, transcript and protein sequence, annotation, and a data report.
The new genome table includes many new features and benefits (see Figure 1). With the new genome table you can:
Figure 1. Conserved Domain Database 
