Uniprot

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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. We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries.

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.

This allows users to get a gene-centric subset of representative proteins for a given genome, as opposed to the full proteome which includes all uniprot e. The number of sequences in UniProtKB has risen to approximately million, uniprot, despite continued work to reduce sequence redundancy at the proteome level. Edde B, 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 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

All materials are free cultural works licensed under a Creative Commons Attribution 4. UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. As the number of completely sequenced genomes continues to increase, huge efforts are being made in the research community to understand as much as possible about the proteins encoded by these genomes. This work is critical to many areas of science including biology, medicine and biotechnology — and is generating a wealth of data. UniProt provides an up-to-date, comprehensive body of protein information. The resource facilitates scientific discovery by collecting, interpreting and organising this information, which saves researchers countless hours of work. You can use UniProt for a wide range of tasks, from finding out about your protein of interest and comparing its protein sequence with other proteins, to mapping a list of identifiers from an external database to UniProtKB or vice versa.

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Figure 8. We are adapting our data input pipeline to ensure that we present a reference proteome for each taxonomic grouping to the research community. Add comment Cancel. There are currently 5, reference proteomes representing a cross-section of the taxonomic diversity found in UniProtKB Figure 2. Evolution biology , Population genetics. Webservice for gene expression and epigenetic data analysis. Upgraded APIs improve computational access to this information. An integrated software for population genetics data analysis. Cunningham F. They are the focus of both manual and automatic annotation, aiming to provide the best annotated protein sets for the selected species. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC , United States.

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.

Growth of automatic annotation rules within UniRule. The UniProt databases exist to support biological and biomedical research by providing a complete compendium of all known protein sequence data linked to a summary of the experimentally verified, or computationally predicted, functional information about that protein. The results table indicates the number of UniProt entries for each proteome and allows users to view or download them in a range of formats. Four annotation types describe different types of amino acid modifications: modified residue, Disulfide bond, Cross-link and Glycosylation. All data is accessible and downloadable using our new programmatic access interface API see below. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. We describe how UniProtKB responded to the COVID pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. New data continue to emerge from methods such as ribosomal profiling which assists with identification of translation start sites, allowing many of these discrepancies to be resolved and improving consistency between the resources. Previously, this dataset only consisted of complete proteomes derived from fully sequenced genomes. Clicking on a feature highlights its position across all tracks so that co-localized elements can be easily identified. Chen C. ISSN