Announcing new links and annotations on Conserved Domain Search results!

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 are will continue to add them as part of our curation effort.

Figure 1 shows the results of an example CD Search showing these new links. Note that you can use the GO and EC information provided to retrieve protein models with these annotations from the Protein Family Models database, for example GO:0030246[GOTermId] — molecular function carbohydrate binding or 2.7.11.1[ECNumber] — non-specific serine/threonine protein kinase.

Figure 1. Conserved Domain Database search results for a hypothetical protein (XP_007132600.1) from the common bean (Phaseolus vulgaris). The results classify the protein as a plant receptor-like protein kinase. The results also show the EC number and the GO terms associated with this domain architecture, a link to a PubMed citation for the protein family (receptor-like protein kinases), and a link to the Domain Architecture Viewer for G-type lectin S-receptor-like serine/threonine-protein kinases. The Domain Architecture Viewer shows other proteins from the NCBI databases with the same domain architecture (order, number and types of domains). Continue reading “Announcing new links and annotations on Conserved Domain Search results!” →

New annotations in RefSeq

In June and July, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-six new annotations in RefSeq for the following organisms:

Anopheles coluzzii (mosquito)
Anopheles funestus (African malaria mosquito)
Astyanax mexicanus (Mexican tetra)
Athalia rosae (coleseed sawfly)
Bactrocera dorsalis (oriental fruit fly)
Brassica napus (rape)
Brienomyrus brachyistius (bony fish)
Canis lupus dingo (dingo) (pictured)
Caretta caretta (Loggerhead turtle)
Dendroctonus ponderosae (mountain pine beetle)
Epinephelus fuscoguttatus (brown-marbled grouper)
Lagopus muta (rock ptarmigan)
Marmota marmota marmota (Alpine marmot)
Nematostella vectensis (starlet sea anemone)
Ostrea edulis (bivalve)
Panthera uncia (snow leopard)
Plutella xylostella (diamondback moth)
Pyrus x bretschneideri (Chinese white pear)
Rhincodon typus (whale shark)
Rhipicephalus sanguineus (brown dog tick)
Solanum stenotomum (eudicot)
Solanum verrucosum (eudicot)
Sphaerodactylus townsendi (lizard)
Stegostoma fasciatum (shark)
Triticum urartu (monocot)
Ziziphus jujuba (common jujube)

Continue reading “New annotations in RefSeq” →

New Features in iCn3D: Expanded Analysis of AlphaFold Structures, Virtual & Augmented Reality

We have added several exciting features to our interactive, web-based 3D-structure viewer, iCn3D! These new features allow you to compare AlphaFold Predicted structures to available structures as well as experience 3D structures with virtual and augmented reality. Learn more about tool updates here.

Continue reading “New Features in iCn3D: Expanded Analysis of AlphaFold Structures, Virtual & Augmented Reality” →

Foreign Contamination Screen (FCS) tool for GenBank submissions

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, rapid detection 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.

Join our mailing list to keep up to date with FCS and other CGR news.

Announcing the NCBI Datasets SARS-CoV-2 taxonomy page

Need SARS-CoV-2 assembled genome sequences or specific SARS-CoV-2 protein sequences? You can find them on the new SARS-CoV-2 taxonomy page brought to you by NCBI Datasets.

The NCBI Datasets SARS-CoV-2 taxonomy page brings you both SARS-CoV-2 genomes and proteins, basic information about SARS-CoV-2, and connections to related NCBI pages, all in one place (see Figures 1 and 2).

Figure 1. NCBI Datasets SARS-CoV-2 taxonomy page. For command-line access, try the datasets command-line tool (top box). For customized filtering options, check out NCBI Virus (bottom box).

If you scroll down the taxonomy page you will find a table of SARS-CoV-2 proteins, each with “Actions” that provide the option to download a package of protein sequences from all annotated SARS-CoV-2 genomes (Figure 2), as well as links to NCBI Gene and the protein sequence from the reference genome.

Figure 2. NCBI Datasets SARS-CoV-2 taxonomy page (cont’d). Click the blue download button to download a package of all SARS-CoV-2 genomes (6 M and counting as of 7/15/22), or just the SARS-CoV-2 reference genome (top box). Below that you see a table of SARS-CoV-2 proteins, each with “Actions” available through the three-dot menu that provides the option to download a package of protein sequences from all annotated SARS-CoV-2 genomes (bottom boxes).

We want to hear from you! Check out the new SARS-CoV-2 taxonomy page and let us know what you think. Contact us with questions or feedback.

Join our mailing list to keep up to date with Datasets and other NCBI news.

RefSeq Release 213

RefSeq Release 213 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 July 11, 2022, and contains 321,282,996 records, including 234,520,053 proteins, 45,781,716 RNAs, and sequences from 121,461 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 213” →

Try out the latest BLAST ClusteredNR database results. Now with in-cluster analyses!

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!

Continue reading “Try out the latest BLAST ClusteredNR database results. Now with in-cluster analyses!” →

NLM’s all-new NCBI Datasets genome table is now available

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:

Find all current genomes, including metagenomes
View multiple taxa such as birds and bees, or polyphyletic groups like fish
Easily find genomes with NCBI RefSeq annotations
Get more accurate genome counts, since each row now represents a single genome with GenBank and RefSeq accessions for that genome in the same row
Customize your downloads to include either GenBank or RefSeq files, or both
Download tables or data packages

Continue reading “NLM’s all-new NCBI Datasets genome table is now available” →

NCBI at 2022 Galaxy Community Conference

Join NCBI’s Nuala O’Leary, PhD at the 2022 Galaxy Community Conference (GCC2022), July 17-23 in Minneapolis, Minnesota, to learn more about Datasets, a new resource that makes it easier to access NCBI sequence data.

GCC2022 brings together hundreds of researchers, trainers, tool developers, software engineers, and computational infrastructure providers, all addressing common challenges in data intensive science using the Galaxy data integration and analysis platform. This will be an in-person meeting with limited support for remote attendees.

Check out NCBI’s schedule of activities:

NCBI Datasets, a new resource for accessing NCBI genome data in Galaxy

Poster: Monday, July 18, 10:20 AM CDT

Talk: Tuesday, July 19, 4:59 PM CDT

Demo: Wednesday, July 20, 10:20 AM CDT

Continue reading “NCBI at 2022 Galaxy Community Conference” →

Introducing the Comparative Genome Viewer (CGV) beta release

NLM’s NCBI is introducing the Comparative Genome Viewer (CGV), an easy-to-use visualization tool that helps you quickly compare eukaryotic genome assemblies and easily identify genomic changes that may be significant to biology and evolution. With the new CGV you can view and compare the alignment between two assemblies to see differences in genomic sequence and structure, including deletions, inversions, and translocations. Currently, you can compare assemblies from over 50 annotated animal and plant genomes.

Continue reading “Introducing the Comparative Genome Viewer (CGV) beta release” →