Uniprot

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely uniprot set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over uniprot last two years to the resource, uniprot. The number of sequences in UniProtKB has risen to approximately million, uniprot, despite continued work to reduce sequence redundancy at the proteome level.

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

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. The manual annotation of an entry involves detailed analysis of the protein sequence and of the scientific literature. Sequences from the same gene and the same species are merged into the same database entry. Differences between sequences are identified, and their cause documented for example alternative splicing , natural variation , incorrect initiation sites, incorrect exon boundaries, frameshifts , unidentified conflicts. Computer-predictions are manually evaluated, and relevant results selected for inclusion in the entry. These predictions include post-translational modifications, transmembrane domains and topology , signal peptides , domain identification, and protein family classification. Relevant publications are identified by searching databases such as PubMed. The full text of each paper is read, and information is extracted and added to the entry. Annotation arising from the scientific literature includes, but is not limited to: [10] [13] [14].

OMArk determines the quality and completeness of gene sets. Annotation arising uniprot the scientific literature includes, but is uniprot limited to: [10] [13] [14], uniprot. Pan proteomes provide a representative set of all the sequences within a taxonomic group and capture unique sequences not found in the group's reference proteome.

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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 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. The UniRef databases cluster sequence sets at various levels of sequence identity and the UniProt Archive UniParc delivers a complete set of known unique sequences, including historical obsolete sequences. Data from selected resources are additionally integrated into UniProtKB records to add biological knowledge and associated metadata enabling the database to act as a central hub from which users can link out to other resources.

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. The proteins expressed in a cell at any moment of time determine its function, its topology, how it reacts to changes in environment and ultimately its longevity and well-being. Improvements in experimental techniques are providing ever deeper information on the structure and function of individual proteins, whilst large-scale sequencing efforts are driving increased coverage of the complete proteomes of the breadth of organisms that populate the tree of life. Our challenge is to capture the growing depth and breadth of information and make it easily available and interpretable to our users.

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Suzek B. Figure 1. Medicinal chemistry , Structural analysis. Panel A shows UniProt annotation for a disulfide bond and an amino acid variation associated with FD that removes the Cystene required for a structural fold. UniRef: comprehensive and non-redundant UniProt reference clusters. Origin, evolution, and maintenance of gene-strand bias in bacteria. This system is freely available for groups to use for in-house protein annotation projects 26 or to contribute their own rules in the URML UniProt Rule Markup Language format which may be reused for the annotation of UniProtKB entries. The UniRef databases cluster sequence sets at various levels of sequence identity and the UniProt Archive UniParc delivers a complete set of known unique sequences, including historical obsolete sequences. MetalPDB in a database of metal sites in biological macromolecular structures. We have, in response to user feedback, re-ordered the presentation of information in the single entry view, grouping information by theme and with the relevant data visualisation view alongside. All of this has been made persistent, so that earlier jobs are automatically stored for a defined period of time. This enables us to leverage the scientific community as a resource for enhancing our curated content, emulating a model already adopted by a number of model organism databases, such as WormBase 40 , PomBase 41 and FlyBase B Taxonomic distribution of unique protein entries that have at least one publication submitted by the community. Montecchi-Palazzi L.

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.

NAR Journals. We have also reviewed and updated our data licencing policies. Fukuda A. With the increasing volume and complexity of our data, we have to make concomitant changes to the way in which we present information to our different user communities and enhance and diversify our search capabilities. ProteomicsDB: a multi-omics and multi-organism resource for life science research. 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. Sayers E. Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. Panel A shows UniProt annotation for a disulfide bond and an amino acid variation associated with FD that removes the Cystene required for a structural fold. Wang E. Interestingly, while polyglutamylation, which consists of the formation of glutamate side chains on specific glutamate residues in the C-terminal tail of both tubulin-alpha and -beta chains, is well-known, the precise positions are still unclear for most proteins. This crowdsourcing activity enables quick access to experimental information on unreviewed entries or those that could benefit from updates, independent of the database release cycle. Archived from the original on 24 September Garcia L. The publications annotated in UniProtKB have previously been displayed in the entry view and a link provided access to a separate page that listed the computationally mapped publications.