Uniprotkb

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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. Annotation is regularly reviewed to keep up with current scientific findings.

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. For our users interested in the accessory proteomes, we have made available sets of pan proteome sequences that cover the diversity of sequences for each species that is found in its strains and sub-strains. To help interpretation of genomic variants, we provide tracks of detailed protein information for the major genome browsers. Protein science is entering a new era that promises to unlock many of the mysteries of the cell's inner workings. Next generation sequencing is transforming the way that we access DNA information and, as the variety of protein assays that can be linked to a DNA or RNA read-out grows, we are gaining protein information at an increasing rate. We are also gaining new insights into the mechanics of large assemblies of proteins through the incredible strides being made in electron microscopy technology. However, this wealth of molecular data will be worth little without it being available to and interpretable by the scientific community. UniProt is a long-standing collection of databases that enable scientists to navigate the vast amount of sequence and functional information available for proteins. For these entries experimental information has been extracted from the literature and organized and summarized, greatly easing scientists access to protein information. These entries are annotated by our rule based automatic annotation systems.

Another important part of the annotation process involves the merging of different reports for a uniprotkb protein, uniprotkb. Figure 4 illustrates our progress in UniRule generation to date.

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.

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.

Uniprotkb

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. The recent rise of big data and high-throughput technologies has shifted a number of paradigms in the scientific community. Although for decades, researchers focused on a single gene and its products, it is now common to work with whole genomes and proteomes.

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UniParc houses all new and revised protein sequences from various sources to ensure that complete coverage is available at a single site. The ProtVista feature viewer. Only residues that satisfy the rule criteria are ultimately propagated to entries within the PIRSF that lack an experimentally derived structure. Download all slides. UniRef is the most comprehensive and non-redundant protein sequence dataset available. Larance M. Finally we provide the UniProt Archive UniParc that provides a complete set of known sequences, including historical obsolete sequences 3. These updates have helped to improve the scalability and usability of UniProt for our end users. The viewing of database entries was improved with configurable views, a simplified terminology and a better integration of documentation. Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase. For our users interested in the accessory proteomes, we have made available sets of pan proteome sequences that cover the diversity of sequences for each species that is found in its strains and sub-strains. UniProt follows a user-centered design process, involving many users worldwide with varied research backgrounds and use cases, to improve its website and add new features.

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

In the course of PTM curation, curators also check that the annotation content of enzymes that mediate modifications is up-to-date. Since our last update in , we have more than doubled the number of reference proteomes to , giving a greater coverage of taxonomic diversity. For the rapid and ongoing accumulation of predicted protein sequences by high-throughput genome sequencing for numerous and increasingly diverse organisms, the expansion of large-scale proteomics e. They are the focus of both manual and automatic annotation, aiming to provide the best annotated protein sets for the selected species. Montecchi-Palazzi L. The biomedical literature is vast, with over one million papers being added to PubMed every year. UniProt Archive UniParc is a comprehensive and non-redundant database, which contains all the protein sequences from the main, publicly available protein sequence databases. Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase. Figure 5. Relevant publications describing the sequencing of the genome are also listed. UniProt follows a user-centered design process, involving many users worldwide with varied research backgrounds and use cases, to improve its website and add new features. The initial GOS dataset is composed of 25 million DNA sequences primarily from oceanic microbes and predicts nearly 6 million proteins.