Uniprotkb

All materials are free cultural works licensed under a Creative Commons Uniprotkb 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, uniprotkb. UniProt curators extract biological information from the literature and perform numerous computational analyses, uniprotkb. Data captured from uniprotkb scientific literature includes information on protein and gene names, function, catalytic activity, cofactors, subcellular location, protein-protein interactions and much more.

Federal government websites often end in. The site is secure. The Universal Protein Resource UniProt provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional value-added information through cross-references to other databases. 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. There is a widely recognized need for a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, integrating and standardizing data from these various sources. UniProt is the central resource for storing and interconnecting information from large and disparate sources, and the most comprehensive catalog of protein sequence 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. 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.

In UniProtKB, annotation consists of the description of the following: function senzyme-specific information, biologically relevant domains and sites, post-translational modifications, subcellular location stissue specificity, developmentally specific expression, structure, interactions, splice isoform sdiseases uniprotkb with deficiencies or abnormalities, uniprotkb, etc. The former contains manually annotated high quality records with information extracted from uniprotkb and curator-evaluated computational analysis.

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

Federal government websites often end in. The site is secure. 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.

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We also provide a series of UniRef databases that provide sequence sets trimmed at various levels of sequence identity 1 , 2. Retrieved 31 March Global subcellular characterization of protein degradation using quantitative proteomics. Contact us. Figure 3. If a proteome is part of a pan proteome, a download link for the pan proteome is also provided. This will eventually cover the ligand space and will enable the identification of conserved motifs and patterns. The sequence of a representative protein, the accession numbers of all the merged entries and links to the corresponding UniProtKB and UniParc records are displayed. UniProt Consortium. Figure 8. UniProt continues to adapt its data gathering, data processing and data display to improve the availability and utility of protein information for the benefit of all. With the growth in biological data, integration and visualization become increasingly important for exposing different data aspects. A pan proteome is the full set of proteins expressed by a group of highly related organisms e.

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.

Only the pathogenic variation in C is annotated in other public resources. The view can be customized to hide or show feature tracks. Species-specific lists of identified experimental peptides from these repositories are uniquely matched to the products of a single gene by comparison with a database of in-silico digested peptides within the target UniProtKB species. Clicking on the conditions highlights the corresponding annotations applied if the conditions hold true and vice versa clicking on the annotations highlights the corresponding conditions. Edde B. Clicking on a feature highlights its position across all tracks so that co-localized elements can be easily identified. Standardized description of scientific evidence using the evidence ontology ECO. Global subcellular characterization of protein degradation using quantitative proteomics. Interestingly, while these modifications have been known for many years, the roles they play are only now starting to be understood. ISSN 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.