Uniprot

Hide the news.

The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically review experimental and predicted data for each protein. The remainder are automatically annotated based on rule systems that rely on the expert curated knowledge. Since our last update in , we have more than doubled the number of reference proteomes to , giving a greater coverage of taxonomic diversity. We implemented a pipeline to remove redundant highly similar proteomes that were causing excessive redundancy in UniProt. The initial run of this pipeline reduced the number of sequences in UniProt by 47 million.

Uniprot

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator ARBA. We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. The UniProt databases exist to support biological and biomedical research by providing a complete compendium of all known protein sequence data linked to a summary of the experimentally verified, or computationally predicted, functional information about that protein. The UniRef databases cluster sequence sets at various levels of sequence identity and the UniProt Archive UniParc delivers a complete set of known sequences, including historical obsolete sequences. UniProt additionally integrates, interprets, and standardizes data from multiple selected resources to add biological knowledge and associated metadata to protein records and acts as a central hub from which users can link out to other resources. The data resource fully supports the Findable, Accessible, Interoperable and Reusable FAIR data principles 2 , for example by making data available in a number of community recognised formats, such as text, XML and RDF and via Application Programming Interfaces API s and File Transfer Protocol FTP downloads, providing stable and traceable identifiers for protein sequence and protein sequence features and by fully evidencing our data sources throughout. We have also reviewed and updated our data licencing policies. UniProt is continually evolving to meet new challenges while still working to capture all available protein sequence data and to curate the ever-increasing amount of functional data described in the scientific literature. In our last update published in this journal in 3 , we described how we are responding to the growth in microbial protein sequence records, largely derived from high-quality metagenomic assembled genomes.

PLoS Biol. Mukhopadhyay A.

Federal government websites often end in. The site is secure. UniProt releases are published every eight weeks. We provide customizable views and downloads in a range of formats via the website, and file sets at the FTP site www. The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content.

All materials are free cultural works licensed under a Creative Commons Attribution 4. UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. As the number of completely sequenced genomes continues to increase, huge efforts are being made in the research community to understand as much as possible about the proteins encoded by these genomes. This work is critical to many areas of science including biology, medicine and biotechnology — and is generating a wealth of data. UniProt provides an up-to-date, comprehensive body of protein information. The resource facilitates scientific discovery by collecting, interpreting and organising this information, which saves researchers countless hours of work.

Uniprot

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator ARBA. We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. The UniProt databases exist to support biological and biomedical research by providing a complete compendium of all known protein sequence data linked to a summary of the experimentally verified, or computationally predicted, functional information about that protein. The UniRef databases cluster sequence sets at various levels of sequence identity and the UniProt Archive UniParc delivers a complete set of known sequences, including historical obsolete sequences.

24 7 anytime fitness

UniProtKB contains decades of literature-based and semi-automated curation describing protein function including variation data In the course of PTM curation, curators also check that the annotation content of enzymes that mediate modifications is up-to-date. In addition to the increased use of structured vocabularies to enhance accessibility to UniProtKB records, we have also improved the presentation of the information within each entry. Figure 6. In the example shown in Figure 3 , detyrosination, acetylation and nitration are supported by experimental evidence and the source references are displayed. These include: enzyme active sites; modified residues; protein binding domains; protein isoforms; protein variations; and more. I agree to the terms and conditions. For tubulin-alpha entries, only one site has been unambiguously identified in mouse. UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. Month: Total Views: November December January February 1, March 2, April 2, May 2, June 2, July 2, August 2, September 2, October 3, November 3, December 2, January 2, February 2, March 3, April 4, May 3, June 2, July 2, August 2, September 2, October 3, November 3, December 2, January 1, February 1, March 1, April 1, May 1, June July August 1, September 1, October 1, November 1, December 1, January 1, February 1, March

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects.

It contains a large amount of information about the biological function of proteins derived from the research literature. Building a pipeline to solicit expert knowledge from the community to aid gene summary curation. Webservice for gene expression and epigenetic data analysis. Researchers are encouraged to add relevant publications to entries of interest to them. Your comment will be reviewed and published at the journal's discretion. Genomics , Transcriptomics. These predictions include post-translational modifications, transmembrane domains and topology , signal peptides , domain identification, and protein family classification. Bansal P. Proteome page for Bacillus subtilis Proteome Res. The results table indicates the number of UniProt entries for each proteome and allows users to view or download them in a range of formats. Yes — manual and automatic. Transcriptomics Systems Biology. Standardized description of scientific evidence using the evidence ontology ECO. Search Menu.