SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, structure of its domains, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.
Full Answer
When was the Swiss-Prot protein sequence data bank developed?
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. [PMID: 9847139]
What is a protein database?
A protein database is one or more datasets about proteins, which could include a protein’s amino acid sequence, conformation, structure, and features such as active sites. Primary databases hold protein sequences inferred from the conceptual translation of the nucleotide sequences.
What are the best online databases for protein and lipid research?
The HAMAP and PROSITE databases of protein families and domains, the ENZYME database of enzyme nomenclature, the SwissLipids database of lipid structures and biological knowledge, the ViralZone portal, and SwissBioPics, a resource of interactive cellular images.
How many amino acids are in Swiss-Prot?
Content of the current SWISS-PROT release Currently (October 1999), SWISS-PROT contains ~81 000 sequence entries, comprising 30 million amino acids abstracted from ~65 000 references. The data file (sequences and annotations) requires 185 Mb of disk storage space.
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.
How do I search Swiss-Prot?
There are multiple sites on the Web that can access the Swiss-Prot/TrEMBL and retrieve the database. Its main sites are the ExPASy Molecular Biology website (http://www.expasy.org/) and the European Institute of Bioinformatics (EBI) website (http://www.ebi.ac.uk/swissprot/).
Is Swiss-Prot A reviewed database?
UniProtKB/Swiss-Prot is now the reviewed section of the UniProt Knowledgebase. The TrEMBL section of UniProtKB was introduced in 1996 in response to the increased dataflow resulting from genome projects.
What is UniProtKB Swiss-Prot database?
UniProtKB/Swiss-Prot is the manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB). It is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.
How are data from SWISS-PROT and TrEMBL different?
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.
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 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.
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.
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.
What are protein databases used for?
In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way.
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.
How many databases does Swiss Prot have?
Currently, SWISS-PROT is linked to 31 different databases and has consolidated its role as the major focal point of bio-molecular databases interconnectivity. In release 38, there is an average of 4.5 cross-references for each sequence entry.
When was SWISS PROT database created?
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
What software is used to retrieve sequence entries?
On both the ExPASy and the EBI Web servers, you can use the Sequence Retrieval System (SRS) (6) software package to query and retrieve sequence entries. The EBI and SIB also offer a range of search services (see http://www2.ebi.ac.uk/ or http://www.expasy.ch/tools/ ) to run Smith–Waterman, FASTA and BLAST sequence similarity searches against SWISS-PROT + TrEMBL.
What 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. SWISS-PROT is now an equal partnership between the EMBL and the Swiss Institute of Bioinformatics (SIB). The EMBL activities are carried out by its Hinxton Outstation, the European Bioinformatics Institute (EBI) (2).
What are the two classes of data in Swiss Prot?
In SWISS-PROT two classes of data can be distinguished: the core data and the annotation. For each sequence entry the core data consists of the sequence data; the citation information (bibliographical references) and the taxonomic data (description of the biological source of the protein), while the annotation consists of the description of the following items:
How many human sequences are annotated in Swiss Prot?
There are currently slightly more than 5400 annotated human sequences in SWISS-PROT. These entries are associated with ~14 500 literature references, 16 000 experimental or predicted PTMs, 800 splice variants and 8000 polymorphisms (most of which are linked with disease states). We will use the current information as the ground basis for what we call the ‘Human Proteomics Initiative’ (HPI).
What are cross references in biomolecular databases?
Cross-references are provided in the form of pointers to information related to SWISS-PROT entries and found in data collections other than SWISS-PROT. For example the sample sequence mentioned above contains, among others, DR (Databank Reference) lines that point to EMBL, PDB, OMIM, Pfam and PROSITE. In this particular example it is therefore possible to retrieve the nucleic acid sequence(s) that codes for that protein (EMBL), the description of genetic disease(s) associated with that protein (OMIM), the 3D structure (PDB) or information specific to the protein family to which it belongs (PROSITE and Pfam).
SWISS-MODEL
is a fully automated protein structure homology-modelling server, accessible via the Expasy web server, or from the program DeepView (Swiss Pdb-Viewer).
Repository
Every week we model all the sequences for thirteen core species based on the latest UniProtKB proteome. Is your protein already modelled and up to date in SWISS-MODEL Repository ?
SARS-CoV-2
Severe acute respiratory syndrome coronavirus 2, is a positive-sense, single-stranded RNA coronavirus. It is a contagious virus that causes coronavirus disease 2019 (COVID-19).
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