Uniprotkb

Federal government websites often end in. The site is secure. The Universal Uniprotkb Resource UniProt provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation, uniprotkb.

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.

Uniprotkb

All materials are free cultural works licensed under a Creative Commons Attribution 4. Expert curation consists of a critical review of experimental and predicted data for each protein by a team of biologists, as well as manual verification of each protein sequence. UniProt curators extract biological information from the literature and perform numerous computational analyses. Data captured from the scientific literature includes information on protein and gene names, function, catalytic activity, cofactors, subcellular location, protein-protein interactions and much more. These entries are largely proteins from species for which we have no experimental data available in the scientific literature. These unreviewed records are enriched with functional annotation by systems using the protein classification tool InterPro , which classifies sequences at superfamily, family and subfamily levels, and predicts the occurrence of functional domains and important sites. Data can be searched in any of the UniProt databases using the methods described below. Once you have found an entry that interests you, click on it to open and you may then scroll down to access all the information within it, either by reading the text or visualising the information in one of the integrated viewers. You can navigate within the entry by clicking on the side-bar. Continue on to the final pages of this online tutorial for recommendations on what to learn next and to tell us what you thought of this tutorial. My learning. My playlists. My account. Contact us. Login Register.

Medini D, uniprotkb. Oxford University Press is a department of the University of Oxford. Search ADS.

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. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC , United States. Each consortium member is heavily involved in protein database maintenance and annotation. The consortium members pooled their overlapping resources and expertise, and launched UniProt in December It combines information extracted from scientific literature and biocurator -evaluated computational analysis.

Federal government websites often end in. The site is secure. Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB. Database URL : www. The human proteome, as we define it in UniProt, is the set of protein sequences that can be derived by translation of all protein-coding genes of the human reference genome, including alternative products such as splice variants. Although curation of human proteins has always constituted the top priority in the UniProt Knowledgebase UniProtKB , the content of the human proteome in UniProtKB has evolved greatly in recent years, partly due to advances in technologies.

Uniprotkb

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.

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The simple addition of a UniProt accession number in a paper could go a long way to helping both UniProt and other resources to incorporate the protein knowledge from new papers into their databases. Expert curation consists of a critical review of experimental and predicted data for each protein by a team of biologists, as well as manual verification of each protein sequence. The tracks can be expanded, as shown in this Figure with the Variants track. To indicate these different levels of evidence for the existence of a protein, we have introduced the PE Protein Existence line to all UniProtKB entries. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. The consortium members pooled their overlapping resources and expertise, and launched UniProt in December Add comment Close comment form modal. Yes — manual and automatic. Vizcaino J. The biomedical literature is vast, with over one million papers being added to PubMed every year. UniProtKB protein entries now have an enhanced view of publications relevant for a protein.

All materials are free cultural works licensed under a Creative Commons Attribution 4.

These include: enzyme active sites; modified residues; protein binding domains; protein isoforms; protein variations; and more. The distribution of proteomes and reference proteomes across the tree of life. Search Menu. In spite of the rise of big data and high-throughput technologies in recent years, which have shifted a number of paradigms in the scientific community, expert curation is by far the most reliable method to report gold-standard information and provide an up-to-date knowledgebase containing experimental information. Searching with ontology terms is assisted by auto-completion, and there is also the possibility of using ontologies to browse search results. Computational biology List of biobanks List of biological databases Molecular phylogenetics Sequencing Sequence database Sequence alignment. It may happen that the protein sequence is not entirely accurate, especially for sequences derived from gene predictions from genomic sequences. UniRef: comprehensive and non-redundant UniProt reference clusters. 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. As the number of new proteomes increases, it is important to organize the data in a way that allows users to effectively navigate the proteomes while keeping relevant and pertinent information easily accessible. ProtVista uses tracks to display different protein features providing an integrated intuitive picture. Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Briefings in Bioinformatics. In the course of PTM curation, curators also check that the annotation content of enzymes that mediate modifications is up-to-date. Read Edit View history.