Uniprot

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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.

Uniprot

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.

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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.

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. The number of sequences in UniProtKB has risen to over million and we are working towards including a reference proteome for each taxonomic group. We continue to extract detailed annotations from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations provided by automated systems using a variety of machine-learning techniques. In addition, the scientific community continues their contributions of publications and annotations to UniProt entries of their interest. The UniProt databases enable the research community to explore the diversity of life as described by the complement of proteins expressed by each organism.

Uniprot

The UniProt Knowledgebase is a collection of sequences and annotations for over million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these proteins. These annotations are supplemented by annotations provided by rule based automated systems, and those imported from other resources. In this article we describe significant updates that we have made over the last 2 years to the resource. We have greatly expanded the number of Reference Proteomes that we provide and in particular we have focussed on improving the number of viral Reference Proteomes. The UniProt website has been augmented with new data visualizations for the subcellular localization of proteins as well as their structure and interactions.

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The card view provides a quick overview of the annotations available for entries in the results e. Oxford University Press is a department of the University of Oxford. Over 30 of these variants have been associated with Mendelian diseases. We are currently redesigning the website to take advantage of new technologies and paradigms in web development and welcome the UniProt user community to participate in user feedback and testing activities by contacting us at help uniprot. Revision received:. Add comment Close comment form modal. Leinonen R. Please check for further notifications by email. Only the pathogenic variation in C is annotated in other public resources. We regularly run webinars, which range from basic introductions to the use of the web pages aimed at new users and students, to more specialist sessions on, for example, use of the API or 3D structural representation in UniProtKB.

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

The accelerating growth of sequenced genomes poses great challenges for databases with their major growth being driven by sequencing of very similar and almost identical strains of the same bacterial species. The UniProt Consortium. On the UniProt website's proteomes pages, you will see a link to download the pan proteome file when a proteome has proteins that are part of a larger pan proteome. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. MacDougall A. Your comment will be reviewed and published at the journal's discretion. Exploring the dark genome: implications for precision medicine. Journal Article. We structured and reannotated binding sites for cognate ligands using ChEBI, and we now use this reference vocabulary for all new ligand binding site annotations. As UniProt is used on a variety of devices, it is essential that our layout adapts to different device screen sizes. Recent advances in the field suggest the existence of a tubulin code, similar to the histone code, with a combination of PTMs that are interpreted by reader proteins UniProtKB integrates large-scale datasets, mapping these data onto the appropriate protein sequence records and displaying the mappings via the ProtVista visualisation tool 28 and downloadable via FTP and APIs Additional visualisations of the subcellular localizations of proteins are now provided in UniProtKB using the web component of SwissBioPics www. 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.