Tag: Protein

Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records

Do you work with or study prokaryotic proteins? As previously announced, we’ve been adding Gene Ontology (GO) terms to RefSeq prokaryotic protein sequence records (example below) to standardize the language when describing the functions of genes and their products. Over 100 million RefSeq proteins from prokaryotes now have at least one GO Term, a 55% increase since we started propagating GO terms from Conserved Domains Database (CDD) architectures in March. Continue reading “Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records” →

Conserved Domain Database version 3.20 is available!

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.

Database statistics for CDD version 3.20:

Models	Source
64,234	Total models from all Source Databases Organized into 4,541 multi-model Superfamilies
18,882	NCBI CDD curation effort
1,125	NCBIfams
1,009	SMART v6.0
19,178	PFAM v34
4,871	COGs v1.0
10,140	NCBI Protein Clusters
4,488	TIGRFAM v15
59,693	Total models form the default CD-Search database

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.

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

Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022

Come visit NCBI at the Bioinformatics Open Science Conference (BOSC), part of the Intelligent Systems for Molecular Biology Conference (ISMB), July 13-16, taking place both in person in Madison, Wisconsin and virtually! We’ll be presenting talks and posters on the latest updates to the NCBI Datasets, BLAST, and Protein resources. You can also join us at the Birds of a Feather (BoF) discussion and the BOSC CollaborationFest (CoFest) to explore these resources and discuss workflows with NCBI staff. Continue reading “Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022” →

NCBI will assign 64-bit numeric GIs by November 15th. Update affected software!

As announced last month, NCBI will begin assigning larger (64-bit) numeric ‘GIs’ to the remaining sequence types that still receive these identifiers. This change is expected as soon as Nov. 15th, 2021 but could occur earlier if data submission volumes are unexpectedly high. This is a reminder that all organizations and developers using our products should review software for any remaining reliance on GIs and compatibility with these larger identifiers.

How do you know if your software or organization may be impacted?

If you have built custom software to interface with NCBI data and consume a sequence database UID (i.e. GI), process the GI from an ASN1 or XML product, or process the GI from any tabular product on FTP, you should review all code to ensure that the new, longer, 64-bit GIs will be handled properly. To ensure a smooth transition and the best overall experience, please update to the latest versions of NCBI-provided programmatic and command line tools. Alternatively, you could make updates to your code to use accession.version identifiers instead of GIs.

NCBI is here to help the community as we make this change. Stay tuned here or follow NCBI Twitter where we will share updates and additional information, such as a final confirmation of the projected cutover date.

Please contact info@ncbi.nlm.nih.gov with any questions about this change or to determine if any software you are using is affected.

Vertebrate Genome Project genome assemblies annotated by NCBI

NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species. See the VGP press release for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank and the European Nucleotide Archive. NCBI has annotated 94 of the VGP assemblies from 85 species using the NCBI Eukaryotic Genome Annotation Pipeline.

These sequence and annotation data are available through NCBI web resources including Gene, Assembly, Nucleotide, Protein, and Datasets and are included in the GenBank and RefSeq releases. You can browse the assemblies in the Genome Data Viewer and download metadata, sequence, and annotation data for the latest assemblies in the VGP BioProject using the NCBI Datasets command-line tools as shown below. Continue reading “Vertebrate Genome Project genome assemblies annotated by NCBI” →

Prokaryotic representative genomes updated — now over 13 thousand assemblies!

We have updated the bacterial and archaeal representative genome collection! The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 11% since August 2020. We’ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and have removed 65 species because of changes in NCBI Taxonomy or uncertainty in their species assignment.

We have also updated the Representative Genomes Database on the Microbial Nucleotide BLAST page as well as the RefSeq Representative Genome Database on basic nucleotide BLAST, to reflect these changes. Continue reading “Prokaryotic representative genomes updated — now over 13 thousand assemblies!” →

The Protein Family Model resource is now available!

The new Protein Family Model resource (Figure 1) provides a way for you to search across the evidence used by the NCBI annotation pipelines to name and classify proteins. You can find protein families by gene symbol, protein function, and many other terms. You have access to related proteins in the family and publications describing members. Protein Family Models includes protein profile hidden Markov models (HMMs) and BlastRules for prokaryotes, and conserved domain architectures for prokaryotes and eukaryotes. The HMMs in the collection include Pfam models, TIGRFAMs as well as models developed at NCBI either de novo, or from NCBI protein clusters. Each of the BlastRules (PMCID: 5753331) consists of one or more model proteins of known biological function with BLAST identity and coverage cutoffs. The conserved domain architectures are based on BLAST-compatible Position Specific Score Matrices (PSSMs) that constitute the NCBI Conserved Domain database.Figure 1. Protein Family Model resource pages. Top panel. Home page. Middle panel, selected results summaries from a fielded search for the DnaK gene product (DnaK[Gene Symbol]). Bottom panel, a portion of an HMM record for DnaK derived from NCBI Protein Clusters (NF009946). The record also includes PubMed citations and HMMER analyses showing the RefSeq proteins named by this method.

Continue reading “The Protein Family Model resource is now available!” →

Updated protein family models used by PGAP available for download

Release 3.0 of the NCBI protein family models used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available from our FTP site. You can search this collection of hidden Markov models (HMMs) against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.

The 3.0 release contains 17,350 models: 12,864 HMMs built at NCBI (111 more than in release 2.0) and 4,486 TIGRFAM HMMs. In addition, since release 2.0, we have assigned product names to over 2,000 Pfam HMMs, bringing the total to 6,698 Pfam HMMs with names that can be transferred by PGAP to the annotated proteins they hit. You can access a table of these product names from the release directory. Prot_evidence Figure 1. The evidence for name assignment for type III secretion system (T3SS) translocon subunit SctB (NF038055) showing the protein matches. Species-specific names for this highly variable component of T3SS include YopD, EspB, IpaC, SipC, etc. Instead, we used the standard moniker for core genes of T3SS, Sct, Secretion and cellular translocation (PMID 26520801, PMID 9618447) providing a unified nomenclature for this secretion system. Continue reading “Updated protein family models used by PGAP available for download” →

Improved access to SARS-CoV-2 data

NCBI Datasets has a simple, new way to get Coronoviridae data, including from SARS-CoV-2 (Figure 1). The data package includes genomic, protein and CDS sequences, annotation and a comprehensive data report for all complete genomes. You can also target your search to major taxonomic ranks within Coronaviridae.

comm-1318_fig1 — Figure 1 – SARS-CoV-2 page within NCBI Datasets showing statistics as of June 16, 2020.

Interested in a specific protein? The SARS-CoV-2 protein page allows you to choose a protein and download the corresponding sequences, annotation and representative structures from all annotated genomes (Figure 2).

comm-1318_fig2 — Figure 2 – SARS-CoV-2 protein page within NCBI Datasets showing annotations on the SARS-CoV-2 reference genome.

Looking for programmatic access? NCBI Datasets offers the same Coronoviridae genomic data and SARS-CoV-2 protein data through a command-line tool and a RESTful API. These tools support additional filtering including the ability to download only those genomes released after a date you specify.

We appreciate your feedback. Try NCBI Datasets and let us know what you think!

New viral protein domain models for annotation of coronaviruses

NLM’s Conserved Domain Database (CDD) has expanded its scope to now include 153 new viral protein domain family models for the annotation of coronaviruses, including models such as for the S1 subunit of coronavirus Spike proteins (cd21527), the nucleocapsid (N) protein of coronavirus (cd21595), and the coronavirus RNA-dependent RNA polymerase (cd21530).

Each curated domain model consists of a multiple sequence alignment containing conserved sequence features that may have been confirmed experimentally, plus links to relevant publications. When available, the domain models include 3D structures with links to interactive 3D views and interacting partners.

Check out this tabular summary of SARS-CoV-2 gene products for links to matching conserved domain models and representative 3D protein structures.

Want to view these alignments in 3D space? We’ve updated iCn3D, a web-based 3D structure viewer, with new rendering, annotation, and alignment features. Read more about how you can use iCn3D to view and analyze SARS-CoV-2-related structures.

Don’t forget to review our SARS-CoV-2 resources page to keep up to date on other coronavirus data at NCBI!