What is the UniProt database?
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.
How do I download data from UniProt?
UniProt is updated every eight weeks (see FAQ on how to be notified automatically of updates ). You can download small data sets and subsets directly from this website by following the download link on any search result page. For downloading complete data sets we recommend using ftp.uniprot.org.
Where can I download the UniProtKB and UniRef databases?
You can download the entire UniProtKB, UniRef and UniParc databases. For downloading these complete data sets, we recommend that you use the UniProt FTP site.
Do I need to upgrade my browser to use UniProt?
Please consider upgrading your browser. When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. More... How can I download data at every UniProt release?
How do I download from UniProt?
You can download small data sets and subsets directly from this website by following the download link on any search result page. For downloading complete data sets we recommend using ftp.uniprot.org.
What is the UniProt database?
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).02-Feb-2021
Is UniProt a primary database?
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects....UniProt.ContentPrimary citationUniProt ConsortiumAccessData formatCustom flat file, FASTA, GFF, RDF, XML.Websitewww.uniprot.org www.uniprot.org/news/16 more rows
How do I download proteome?
Go to the UniProt website and click on the search selection drop-down (Figure 60): Figure 60 Dataset selection drop-down. Select 'Proteomes', type Escherichia coli and click on the looking search icon (Figure 61): Figure 61 Proteomes search for 'Escherichia Coli'.
Is UniProt and Swiss-Prot same?
UniProtKB/TrEMBL is a computer-annotated (unreviewed) supplement to Swiss-Prot, which strives to gather all protein sequences that are not yet represented in Swiss-Prot.
How reliable is UniProt?
UniProtKB encompasses several individual protein sequence resources that are depicted on this page. If you are talking about a sequence that is from SwissProt (manually reviewed/curated sequences) or UniRef100 clusters then that sequence is likely perfectly accurate.26-Oct-2018
Why do we use UniProt?
UniProt helps with this in the following ways: It provides an up-to-date, comprehensive body of protein information at a single site. It aids scientific discovery by collecting, interpreting and organising this information so that it is easy to access and use. ... It provides tools to help with protein sequence analysis.
Is UniProt curated?
Accurate and comprehensive representation of biological knowledge, as well as easy access to this data for working scientists and a basis for computational analysis, are primary goals of biocuration. In order to respond to the flood of sequencing data, UniProt provides both manual curation and automatic annotation.14-May-2021
How large is 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.28-Nov-2016
How many proteins are in UniProt?
UniProt release 2020_04 contains over 189 million sequence records (Figure 1), with >292 000 proteomes, the complete set of proteins believed to be expressed by an organism, originating from completely sequenced viral, bacterial, archaeal and eukaryotic genomes available through the UniProtKB Proteomes portal (https:// ...25-Nov-2020
How many proteomes are there in the UniProt database?
1) approximately 20,000 human protein-coding genes represented by the canonical protein sequence in UniProtKB/Swiss-Prot: Query: proteome:up000005640 AND reviewed:yes.06-Dec-2019
What cell has a proteome?
The genomes of viruses and prokaryotes encode a relatively well-defined proteome as each protein can be predicted with high confidence, based on its open reading frame (in viruses ranging from ~3 to ~1000, in bacteria ranging from about 500 proteins to about 10,000).
What is a UniProtKB?
UniProtKB is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. It consists of two sections: 1 Reviewed (Swiss-Prot) – contains manually annotated records 2 Unreviewed (TrEMBL) – contains computationally analysed records
What is a Uniparc database?
UniParc is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world. UniParc stores each unique sequence only once, giving it a stable and unique identifier (UPI).
How is UniRef90 made?
UniRef90 is built by clustering UniRef100 sequences such that each cluster is composed of sequences that have at least 90% sequence identity to the longest sequence (the seed sequence) of the cluster . UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to the longest sequence in the cluster.
What is UniProt database?
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.
What is the purpose of UniProt Knowledgebase?
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 190 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. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
How often is UniProt released?
Due to the ever-increasing number of sequence records UniProt is processing with every release cycle, as of release 2020_01 (26 February 2020), UniProt releases are now published every eight weeks. This gives our production team the time required to complete data import, proteome redundancy removal, data checking, integration of external data and automatic annotation of unreviewed records prior to starting the release process.
How many proteomes are there in UniProt?
UniProt release 2020_04 contains over 189 million sequence records (Figure 1 ), with >292 000 proteomes, the complete set of proteins believed to be expressed by an organism, originating from completely sequenced viral, bacterial, archaeal and eukaryotic genomes available through the UniProtKB Proteomes portal ( https://www.uniprot.org/proteomes/ ). The majority of these proteomes continue to be based on the translation of genome sequence submissions to the INSDC source databases—ENA, GenBank and the DDBJ ( 4 )—supplemented by genomes sequenced and/or annotated by groups such as Ensembl ( 5 ), NCBI RefSeq ( 6 ), Vectorbase ( 7) and WormBase ParaSite ( 8 ). Viral proteomes are manually checked and verified and periodically added to the database.
What is UniProt working on?
UniProt is continually evolving to meet new challenges while still working to capture all available protein sequence data and to curate the ever-increasing amount of functional data described in the scientific literature.
What is the role of Uniprot?
UniProt continues to play its pivotal role in the fields of biology and biomedicine, collecting, standardizing and organizing knowledge of proteins and their functions to create a reference framework for multiscale biomedical data integration and analysis. Organisms are being routinely sequenced at the whole genome level, and eukaryotic, prokaryotic, and metagenomic sequencing projects are all contributing to the increased diversity of sequence data in the UniProt databases. It is of increasing importance that our automatic annotation pipelines continue to develop in parallel to ensure that these unreviewed genomes, the vast majority of which are not being experimentally studied at the protein level, are richly and comprehensively annotated with functional information. Expert curation of those proteins biochemically characterized remains a key focus of our activities, to both inform on these well-studied entities and also to act as template entries for information transfer to proteins in related species. As the complexity and depth of our value-added data increases, we are exploring new ways to present the data to users and will continue to serve the community with new and improved website access designed to improve and enhance the user experience and upgraded programmatic access, with ease of use always a priority.
What is the purpose of a single protein sequence?
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 proteins (e.g. including isoforms) that map to the genome. Figure 2.