Who maintains Swiss-Prot?
1. Swiss-Prot and TrEMBL. SWISS-PROT is a protein sequence database containing detailed annotations. It was established in 1986 and jointly maintained by the department of medical biochemistry of the University of Geneva and the EMBL data library (now EBI) since 1987.
What is Swiss-Prot database?
SWISS-PROT (1) is an annotated protein sequence database, which was created at the Department of Medical Biochemistry of the University of Geneva and has been a collaborative effort of the Department and the European Molecular Biology Laboratory (EMBL), since 1987.
What is Swiss-Prot Wikipedia?
UniProtKB/Swiss-Prot is a manually annotated, non-redundant protein sequence database. It combines information extracted from scientific literature and biocurator-evaluated computational analysis.
Is Swiss-Prot and UniProt same?
Swiss-Prot (created in 1986) is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. UniProtKB/Swiss-Prot is now the reviewed section of the UniProt Knowledgebase.
When was SWISS-PROT established?
SWISS-PROT ( 1 ) is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1987, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library (now the EMBL Outstation-The European Bioinformatics Institute; 2 ).
Is SWISS-PROT a secondary database?
Complete answer: SWISS PROT is a protein sequence database. Annotations in the database provide all the information regarding the structure and function of a particular protein along with its functions and modifications if any. The data is all primary and easily accessible.
What is the difference between Swiss Prot and TrEMBL?
TrEMBL consists of entries in a SWISS-PROT format that are derived from the translation of all coding sequences in the EMBL nucleotide sequence database, that are not in SWISS-PROT. Unlike SWISS-PROT entries those in TrEMBL are awaiting manual annotation.
Which is the best annotated database?
Among all protein sequence databases, UniProt (UniProt Consortium, 2011) is the most widely used one. It provides more annotations than any other sequence database with a minimal level of redundancy through human input or integration with other databases.
Who created UniProt?
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.
Is Swiss-Prot manually annotated?
The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms.
What is UniProt used for?
UniProt is the central resource for storing and interconnecting information from large and disparate sources, and the most comprehensive catalog of protein sequence and functional annotation.
What is Swissport in bioinformatics?
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.
What is UniProt used for?
UniProt is the central resource for storing and interconnecting information from large and disparate sources, and the most comprehensive catalog of protein sequence and functional annotation.
What is Entrez database?
Entrez is a molecular biology database system that provides integrated access to nucleotide and protein sequence data, gene-centered and genomic mapping information, 3D structure data, PubMed MEDLINE, and more.
What is EMBL database?
The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/index.html ) is a comprehensive collection of primary nucleotide sequences maintained at the European Bioinformatics Institute (EBI).
What are protein sequence databases?
A protein database is a collection of data that has been constructed from physical, chemical and biological information on sequence, domain structure, function, three‐dimensional structure and protein‐protein interactions. Collectively, protein databases may form a protein sequence database.
What is Swissport International?
Swissport International Ltd. is an aviation services company providing airport ground and cargo handling services owned by an international group of investors. It is headquartered in Opfikon, Switzerland. It handles around 282 million passengers and 4.8 million tonnes of cargo annually, on behalf of some 850 client-companies in the aviation sector.
When was Swissport founded?
The company was founded in 1996 as Swissair Ground Services International, independent of the former Swissair. In the following years, the company expanded both through organic growth and through various acquisitions. As part of the Swissair financial crisis, Swissport was first purchased by the British private equity firm Candover Investments and in August 2005 by the Spanish construction company Ferrovial. In the meantime, the company has grown through various acquisitions. At the end of 2010, Ferrovial sold Swissport for €654 million to the French private equity firm PAI Partners.
When did Swissport cut its workforce?
On June 25, 2020, Swissport UK & Ireland announced to cut a workforce of 8,500 by 50%. In December 2020, Swissport had completed its comprehensive financial restructuring that began in August 2020.
Who bought Swissport?
As part of the Swissair financial crisis, Swissport was first purchased by the British private equity firm Candover Investments and in August 2005 by the Spanish construction company Ferrovial. In the meantime, the company has grown through various acquisitions.
Is Swissport a 100% shareholder in Aerocare?
Swissport now holds 100% of Aerocare, the leading Aviation Services and Airport Infrastructure Services provider in Australia/ New Zealand. On June 8, 2020, Swissport's Belgian subsidiary declared bankruptcy, which was confirmed by the Belgian commercial courts the following day.
When did Swiss-Prot go through a funding crisis?
Swiss-Prot in particular went through a major funding crisis in 1996, which led the leaders of the five research groups active in bioinformatics in Geneva and Lausanne, Ron Appel, Amos Bairoch, Philipp Bucher, Victor Jongeneel and Manuel Peitsch to create SIB. Once created, the institute could then apply for funding under a Swiss law ...
What is SIB Swiss?
sib .swiss. The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland . The institute was established on 30 March 1998 and its mission is to provide core bioinformatics resources to the national and international life science research community in fields such ...
What is SIB in bioinformatics?
SIB manages several bioinformatics core facilities that provide informatics and statistical support, as well as services and advice to life scientists, thus enabling them to conduct their research projects and analyse the resulting data. Core facilities have been set up for genomics, transcriptomics and proteomics research. SIB also maintains the Vital-IT High Performance Computing Centre that provides computational resources, development support and consultancy to the Swiss life science community both in academia and industry. The Vital-IT infrastructure is distributed to three sites: University of Lausanne, EPFL and University of Geneva. Compute resources and bioinformatics expertise are also provided in the Basel area with sciCORE, the Basel Computational Biology Center.
Who was the first director of the SIB?
The first director of the institute was Victor Jongeneel followed by Ernest Feytmans between 2001 and September 2007. From 1 October 2007 until July 2018, the institute was led by Ron Appel, one of its founding members. Since July 2018, the SIB is led by Christine Durinx and Ron Appel, as Joint Executive Directors.
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.
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 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.
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.
Where is PIR located?
PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Georgetown University Medical Center in Washington, DC, US, is heir to the oldest protein sequence database, Margaret Dayhoff 's Atlas of Protein Sequence and Structure, first published in 1965.
When was Swiss Prot created?
Swiss-Prot, the manually annotated protein sequence database, was born! This was in 1986. At that time, the various versions were distributed on magnetic tapes by EMBL-Heidelberg. It was the start of a long-lasting collaboration.
What is UniProt Knowledgebase?
In this context, the UniProt Knowledgebase (UniProtKB) was created, consisting in the curated UniProtKB/Swiss-Prot databank, its automatically annotated supplement TrEMBL, and the PIR protein database 5. Today, UniProtKB represents the world's most comprehensive catalogue of information on proteins1. In the space of 30 years, the number of proteins entered in UniProtKB/Swiss-Prot has risen from 4,000 to 550,000, and the staff from one to 70 people 6 of whom 50 are in Geneva.
When was SIB created?
To solve the issue, the SIB Swiss Institute of Bioinformatics was created in 1998: the Geneva Swiss-Prot group had a new home and its mission was to keep on developing the database. The collaboration with the team in EMBL-EBI could continue 2.
Pipeline
SWISS-MODEL pipeline comprises the four main steps that are involved in building a homology model of a given protein structure:
Workspace
The SWISS-MODEL Workspace integrates programs and databases required for protein structure modelling in a web-based workspace.
Repository
The SWISS-MODEL Repository provides access to an up-to-date collection of annotated three-dimensional protein models for a set of model organisms of high general interest. Model organisms include human, mouse, C.elegans, E.coli, and various pathogens including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Accuracy and reliability of the method
In the past, the accuracy, stability and reliability of the SWISS-MODEL server pipeline was validated by the EVA-CM benchmark project.
Overview
History
The institute was originally created to provide a framework for stable long-term funding for both the Swiss-Prot database and the Swiss EMBnet node. Swiss-Prot in particular went through a major funding crisis in 1996, which led the leaders of the five research groups active in bioinformatics in Geneva and Lausanne, Ron Appel, Amos Bairoch, Philipp Bucher, Victor Jongeneel and Manuel Peitsch to create SIB. Once created, the institute could then apply for funding under a Swiss law …
Organisation
The SIB Swiss Institute of Bioinformatics is a federation of research groups with affiliated bioinformaticians at 21 SIB partner institutions, including the Universities of Basel, Bern, Fribourg, Geneva, Lausanne, Lugano and Zurich, the Federal Institutes of Technology in Lausanne and Zurich, the Friedrich Miescher Institute for Biomedical Research, the Institute of Oncology Research in Bellinzona, and the Geneva School of Business Administration (HEG). Current research groups i…
Bioinformatics resources
The institute offers a wide range of resources for the life science research community, most being open and accessible through Expasy, the SIB bioinformatics resource portal. They include:
SIB develops and maintains databases of international standing, including UniProtKB/Swiss-Prot (curated protein sequence database providing a high level of annotation), neXtProt (human-centric protein knowledge platform), SWISS-MODEL Repository (three-dimensional protein structure mod…
Education and training
One of SIB’s priorities is to promote and coordinate education in bioinformatics. SIB members are directly, or indirectly, involved in a number of bioinformatics courses at all educational levels – from high school to undergraduate and graduate degrees – as well as in specialized training for life scientists. SIB also promotes a PhD Training Network in bioinformatics, which is open to graduate students at Swiss schools of higher education. The objectives of this network are two-…
Popular science
The SIB is also involved in bringing bioinformatics to the layman. Understanding the growing importance this relatively recent science has in today’s society is becoming fundamental. Indeed, in not too distant a future, patients will be referring to results directly generated by bioinformatics methods. Since the year 2000, in order to heighten public awareness, the SIB has taken part in numerous science fairs, created two online magazines, an outdoor exhibition and, in 2012, a virt…
See also
• Lausanne campus
• List of biological databases
• Science and technology in Switzerland
External links
• Official website
• Swiss Bioinformatics Resource Portal (Expasy)
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 b...
The UniProt consortium
- The UniProt consortium comprises the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, and the Protein Information Resource. 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 servers that are a central resource for prot…
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. These databases coexisted with differing protein sequence coverage and annotation priorities. Swiss-Prot was created in 1986 by Amos Bairoch …
Organization of UniProt databases
- UniProt provides four core databases: UniProtKB, UniParc, UniRef.
Funding
- UniProt is funded by grants from the National Human Genome Research Institute, the National Institutes of Health, the European Commission, the Swiss Federal Government through the Federal Office of Education and Science, NCI-caBIG, and the US Department of Defense.