Tag: Comparative Genomics Resource (CGR)

Announcing new links and annotations on Conserved Domain Search results!

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

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”

Foreign Contamination Screen (FCS) tool for GenBank submissions

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.

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

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

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

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

Introducing the Comparative Genome Viewer (CGV) beta release

Try out Datasets and ElasticBLAST at the BOSC 2022 CoFest!

Try out Datasets and ElasticBLAST at the BOSC 2022 CoFest!

Join NLM’s NCBI at the virtual CollaborationFest on July 15 from 08:00 – 11:00 CDT and 12:00 – 16:00 CDT following the BOSC 2022 conference. Get an in-depth orientation and opportunity to test the capabilities of Datasets and ElasticBLAST.

What is Datasets?

Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download gene, transcript, protein and genome sequences, annotation and metadata. We invite you to try the Datasets command line tool in your bioinformatic workflows! Continue reading “Try out Datasets and ElasticBLAST at the BOSC 2022 CoFest!”

Introducing NLM’s new NCBI Datasets genome page!

Introducing NLM’s new NCBI Datasets genome page!

As part of an ongoing effort to modernize and improve your experience, NLM’s NCBI Datasets is introducing all-new genome pages. These pages make it easier for you to browse and download genome sequence and metadata, and navigate to tools such as the Genome Data Viewer (GDV) and BLAST.

To get started, search NCBI Datasets by assembly accession (e.g., GCF_016699485.2), assembly name (e.g., bGalGal1.mat.broiler.GRCg7b), WGS accession (e.g., JAENSK01), or species name + genome (e.g., chicken genome), and click on the title in the box. See the top red arrow in Figure 1 below where we search for ‘chicken genome’.

Figure 1: Finding the chicken reference assembly. A search for ‘chicken genome’ returns a box that provides a quick link to the new genome page (middle red arrow). From there, the download button (bottom red arrow) allows you to select the files you need (see ‘Download Package’ window on the left) along with a detailed metadata report that includes all the metadata on the web page.  Continue reading “Introducing NLM’s new NCBI Datasets genome page!”

New RefSeq annotations are available!

New RefSeq annotations are available!

In April and May, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-eight new annotations in RefSeq for the following organisms: