What is Swiss Prot?
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's new in the Swiss-Prot database?
Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT.
Who is responsible for the UniProt database?
It is handled by the Universal Protein Resource Consortium (UniProt) (earlier maintained by Swiss Institute of Bioinformatics, Switzerland, and EBI), and since 1988, it has also been overseen by the Department of Medical Biochemistry, University of Geneva, and EMBL Data Library ( Bairoch and Boeckmann, 1991 ).
What are the UniProt reference clusters?
The UniProt Reference Clusters (UniRef) consist of three databases of clustered sets of protein sequences from UniProtKB and selected UniParc records.
Which is a primary protein database?
Protein Databank (PDB): PDB is a primary protein structure database. It is a crystallographic database for the three-dimensional structure of large biological molecules, such as proteins.
Is SWISS-PROT a nucleotide sequence database?
The SWISS-PROT protein sequence data bank consists of sequence entries. Sequence entries are composed of different line types, each with their own format. For standardization purposes the format of SWISS-PROT ( 3 ) follows as closely as possible that of the EMBL nucleotide sequence database.
What are the primary databases?
Primary databases are also called as archieval database. They are populated with experimentally derived data such as nucleotide sequence, protein sequence or macromolecular structure. Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature.
Is TrEMBL primary database?
TrEMBL database (primary databases)
What type of database is SWISS-PROT?
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 Swissport database?
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.
Which is a secondary database?
A database that provides an alternative set of keys to access that data is called a secondary database. In a secondary database, the keys are your alternative (or secondary) index, and the data corresponds to a primary record's key.
What are primary database and secondary database?
Primary databases store and make data available to the public, acting as repositories. Secondary databases make use of publicly available sequence data in primary databases to to provide layers of information to DNA or protein sequence data.
Which of the following is secondary database?
OMIM is a secondary database consists of data derived from the analysis of primary data such as sequences, active site residue of proteins and so on. Thus the correct answer is option C.
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 Prosite a secondary database?
PROSITE and PRINTS are the only manually annotated secondary databases. The print is a diagnostic collection of protein fingerprints.
Is RefSeq a secondary database?
No, both records will continue to be available. RefSeq and GenBank (a member of the INSDC) are separate databases, and both databases are available at NCBI.
Focus on the group's mission
The Swiss-Prot team excels in the art of generating machine-readable knowledge of biology from the ever growing body of scientific publications. It is harnessing the power of deep learning to accelerate literature triage and information extraction, thus delivering the most accurate and informative evidence to users in a timely manner.
Biocuration and software development
We organize, clean & control the quality of your datasets for subsequent analysis. In addition, we can process, transform and align your datasets to existing standards and make them available as a database. We can propose different data storage solutions depending on project needs (e.g. federated versus integrated).
Supporting AI with machine-readable biological knowledge
Knowledgebases like UniProtKB are an essential part of the AI ecosystem; the collective biological knowledge they contain, in the form of pathways, ontologies and networks, can be used to create generalizable and interpretable models that reveal actionable biological mechanisms.
Publications
Parit Bansal, Anne Morgat, Kristian B Axelsen, Venkatesh Muthukrishnan, Elisabeth Coudert, Lucila Aimo, Nevila Hyka-Nouspikel, Elisabeth Gasteiger, Arnaud Kerhornou, Teresa Batista Neto, Monica Pozzato, Marie-Claude Blatter, Alex Ignatchenko, Nicole Redaschi, Alan Bridge. Rhea, the reaction knowledgebase in 2022.
Proteins
SWISS-PROT (Bairoch and Apweiler, 1996) 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.
From molecules to patients: the clinical applications of biological databases and electronic health records
Ayyagari Ramlal, ... Rubina Chongtham, in Translational Bioinformatics in Healthcare and Medicine, 2021
IFNα and IFNω
Katherine A. Fitzgerald, ... Robin E. Callard, in The Cytokine FactsBook and Webfacts (Second Edition), 2001
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.
Focus on The group's Mission
- The Swiss-Prot team excels in the art of generating machine-readable knowledge of biology from the ever growing body of scientific publications. It is harnessing the power of deep learning to accelerate literature triage and information extraction, thus delivering the most accurate and informative evidence to users in a timely manner.
Biocuration and Software Development
- Our team of biocurators and software developers annotate, maintain and develop a range of internationally renowned expert-curated knowledge resources: 1. Two ELIXIR Core Data Resources: UniProtKB/Swiss-Prot protein sequence database, the most widely used protein information resource in the world, and the Rheadatabase of biochemical reactions 2. The HAMA…
Supporting Ai with machine-readable Biological Knowledge
- Knowledgebases like UniProtKB are an essential part of the AI ecosystem; the collective biological knowledge they contain, in the form of pathways, ontologies and networks, can be used to create generalizable and interpretable models that reveal actionable biological mechanisms. Find out more about the Group’s activities