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.
What is the UniProt KnowledgeBase biocuration?
One of the central activities of the UniProt Consortium is the biocuration of the UniProt Knowledgebase (UniProtKB). Biocuration involves the interpretation and integration of information relevant to biology into a database or resource that enables integration of the scientific literature as well as large data sets.
Who produces UniProt?
Who produces UniProt? UniProt is produced by the UniProt Consortium (Figure 1), a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR).
Why UniProt protein data?
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.
Is UniProt supported by the NIH or NSF?
PIR's UniProt activities are also supported by the NIH grants R01GM080646, G08LM010720, and P20GM103446, and the National Science Foundation (NSF) grant DBI-1062520. UniProt has been supported by the NIH grants U01HG02712 (2002-2010) and U41HG006104 (2010-2014).
What is the function of 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.
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.
What is UniProt annotation?
UniProt uses InterPro to classify sequences at superfamily, family and subfamily levels and to predict the occurrence of functional domains and important sites. InterPro integrates predictive models of protein function, so-called 'signatures', from a number of member databases.16-Jul-2020
What is a UniProt number?
An accession number (AC) is assigned to each sequence upon inclusion into UniProtKB. Accession numbers are stable from release to release. If several UniProtKB entries are merged into one, for reasons of minimizing redundancy, the accession numbers of all relevant entries are kept.10-Apr-2018
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
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
What are the components of UniProt consortium?
UniProt is comprised of four major components, each optimized for different uses: the UniProt Knowledgebase, the UniProt Reference Clusters, the UniProt Archive and the UniProt Metagenomic and Environmental Sequences database.
What is a Psi Blast?
PSI-BLAST (Position-Specific Iterative Basic Local Alignment Search Tool) derives a position-specific scoring matrix (PSSM) or profile from the multiple sequence alignment of sequences detected above a given score threshold using protein–protein BLAST.
What is genomic sequence annotation?
Genome annotation is the process of identifying functional elements along the sequence of a genome, thus giving meaning to it. It is necessary because the sequencing of DNA produces sequences of unknown function.
Is UniProt a secondary database?
Hybrid databases and families of databases Many data resources have both primary and secondary characteristics. For example, UniProt accepts primary sequences derived from peptide sequencing experiments.
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 often is UniProt released?
every 8 weeksUniProt releases are published every 8 weeks (4 weeks until the last 2019 release, 2019_11), with possible exceptions in January and summer due to reduced staff during holidays.26-Jan-2021
What is UniProt database?
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.
Who is Uniprot funded by?
UniProt is funded by grants from the National Human Genome Research Institute, the National Institutes of Health (NIH), the European Commission, the Swiss Federal Government through the Federal Office of Education and Science, NCI-caBIG, and the US Department of Defense.
What is a UniProt reference cluster?
The UniProt Reference Clusters (UniRef) consist of three databases of clustered sets of protein sequences from UniProtKB and selected UniParc records. The UniRef100 database combines identical sequences and sequence fragments (from any organism) into a single UniRef entry. 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. UniRef100 sequences are clustered using the CD-HIT algorithm to build UniRef90 and UniRef50. Each cluster is composed of sequences that have at least 90% or 50% sequence identity, respectively, to the longest sequence. Clustering sequences significantly reduces database size, enabling faster sequence searches.
What is UniProt consortium?
The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services.
Why does Uniparc only store one sequence?
In order to avoid redundancy, UniParc stores each unique sequence only once. Identical sequences are merged, regardless of whether they are from the same or different species. Each sequence is given a stable and unique identifier (UPI), making it possible to identify the same protein from different source databases.
When was Swiss Prot created?
Swiss-Prot was created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinformatics and subsequently developed by Rolf Apweiler at the European Bioinformatics Institute.
What is Swiss Prot?
UniProtKB/Swiss-Prot is a manually annotated, non-redundant protein sequence database. It combines information extracted from scientific literature and biocurator -evaluated computational analysis. The aim of UniProtKB/Swiss-Prot is to provide all known relevant information about a particular protein. 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.
What is Uniprot in science?
UniProt provides an up-to-date, comprehensive body of protein information.
Who makes UniProt?
Who produces UniProt? UniProt is produced by the UniProt Consortium (Figure 1), a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR).
What is 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). The UniProt consortium and host institutions EMBL-EBI, SIB and PIR are committed to the long-term preservation of the UniProt databases.
What is Uniprot EBI?
UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR). Across the three institutes more than 100 people are involved through different tasks such as database curation, software development and support.
Who is the head of Uniprot?
The UniProt consortium is headed by Alex Bateman, Alan Bridge and Cathy Wu, supported by key staff, and receives valuable input from an independent Scientific Advisory Board.
What is UniProt Knowledgebase?
One of the central activities of the UniProt Consortium is the biocuration of the UniProt Knowledgebase (UniProtKB). Biocuration involves the interpretation and integration of information relevant to biology into a database or resource that enables integration of the scientific literature as well as large data sets. 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. UniProtKB consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. The former contains manually reviewed records with annotation extracted from the literature and curator evaluated computational analysis while the latter contains computationally generated records enhanced by automatic classification and annotation.
What is UniProt ARBA?
UniRule is a collection of manually curated annotation rules which define annotations that can be propagated based on specific conditions while the Association-Rule-Based Annotator (ARBA) is an automatic decision-tree based rule-generating system. The central components of these approaches are rules based on InterPro classification and the manually curated data in UniProtKB/Swiss-Prot. More...
Overview
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 foundat…
The UniProt consortium
The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by t…
The roots of UniProt databases
Each consortium member is heavily involved in protein database maintenance and annotation. Until recently, EBI and SIB together produced the Swiss-Prot and TrEMBL databases, while PIR produced the Protein Sequence Database (PIR-PSD). These databases coexisted with differing protein sequence coverage and annotation priorities.
Swiss-Prot was created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Insti…
Organization of UniProt databases
UniProt provides four core databases: UniProtKB (with sub-parts Swiss-Prot and TrEMBL), UniParc, UniRef.
UniProt Knowledgebase (UniProtKB) is a protein database partially curated by experts, consisting of two sections: UniProtKB/Swiss-Prot (containing reviewed, manually annotated entries) and UniProtKB/TrEMBL (containing unreviewed, automatically annotated entries). As of 19 March 20…
Funding
UniProt is funded by grants from the National Human Genome Research Institute, the National Institutes of Health (NIH), the European Commission, the Swiss Federal Government through the Federal Office of Education and Science, NCI-caBIG, and the US Department of Defense.
External links
• UniProt
Funding
- UniProt is supported by the National Eye Institute (NEI), National Human Genome Research Institute (NHGRI), National Heart, Lung, and Blood Institute (NHLBI), National Institute on Aging (NIA), National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of General Medical Sciences (NIG…
Past Funding
- UniProt has been supported by the NIH grants U01HG02712 (2002-2010) and U41HG006104 (2010-2014). UniProt activities at EMBL-EBI have benefited from the FP7 SLING project (2009-2012, contract number 226073), British Heart Foundation grants SP/07/007/23671 and RG/13/5/30112, the Parkinson's Disease United Kingdom GO grant G-1307 and the NIH GO grant …
Further Information
Contact The Uniprot Consortium Members
- European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Phone: (+44 1223) 494 444 Fax: (+44 1223) 494 468 SIB Swiss Institute of Bioinformatics Centre Medical Universitaire 1, rue Michel Servet 1211 Geneva 4 Switzerland Phone: (+41 22) 379 50 50 Fax: (+41 22) 379 58 58 Protein Information ...