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.
Is Swiss-Prot a primary database?
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.
Is Swiss-Prot A reviewed database?
SWISS-PROT database contains the protein sequences that have been carefully examined and accurately annotated in the EMBL nucleic acid sequence database.
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 ).
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.
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.
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.
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 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 does UniProt stand for?
The Universal Protein ResourceThe 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).
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:// ...
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.
When was TrEMBL release 11 released?
In July 1999 , TrEMBL release 11 was produced. Release 11 was based on the translation of all 379 000 CDSs in the EMBL Nucleotide Sequence Database release 58. Around 119 000 of these CDSs were already as sequence reports in SWISS-PROT and thus excluded from TrEMBL. The remaining 260 000 sequence entries have been automatically merged whenever possible to reduce redundancy in TrEMBL. This step has led to 245 761 TrEMBL entries.
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 is TrEMBL in computer?
TrEMBL: A COMPUTER ANNOTATED SUPPLEMENT TO SWISS-PROT
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.
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:
When was SWISS PROT database created?
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
What is the UniProt Knowledgebase?
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data.
Why are all protein sequences encoded by the same gene merged into a single sequence?
In order to have minimal redundancy and to improve sequence reliability , all protein sequences encoded by a same gene are merged into a single UniProtKB/Swiss-Prot entry. Differences found between various sequencing reports are analysed and fully described in the feature table (alternative splicing events, genetic variations or conflicts for example). Once in UniProtKB/Swiss-Prot, a protein entry is removed from UniProtKB/TrEMBL.
What is manual annotation?
Manual annotation consists of a critical review of experimentally proven or computer-predicted data about each protein, including the protein sequences. Data are continuously updated by an expert team of biologists.
Can you use the basket to save UniProt proteins?
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.
How many TREMBL pre-entries are there?
Translation of all CDS in the EMBL nucleotide sequence database release 44 resulted in the creation of 145 000 TREMBL pre-entries. Around 65 000 of these pre-entries were already present as sequence reports in SWISS-PROT and were excluded from TREMBL. The remaining ∼80 000 sequence entries have been automatically merged whenever possible, to reduce redundancy in TREMBL. This step led to ∼70 000 TREMBL entries, which supplement SWISS-PROT.
Why is tREMBL used in SWISS PROT?
The creation of TREMBL as a supplement to SWISS-PROT was not only for the purpose of producing a more complete and up to date protein sequence collection. We used this task to also achieve a deeper integration of the EMBL nucleotide sequence database with SWISS-PROT + TREMBL.
What is Swiss Prot?
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 domain structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to seven additional databases; a variety of new documentation files; the creation of TREMBL, an unannotated supplement to SWISS-PROT. This supplement consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except CDS already included in SWISS-PROT.
How much space does SWISS PROT use?
Release 32.0 of SWISS-PROT (October 1995) contains 48 440 sequence entries, comprising 17 000 000 amino acids abstracted from ∼43 000 references. The data file (sequences and annotations) requires 90 Mb disk storage space. The documentation and index files require ∼30 Mb disk space. No restrictions are placed on use or redistribution of the data.
How many databases does Swiss Prot have?
Currently, SWISS-PROT is linked to 24 different databases and has consolidated its role as the major focal point of biomolecular database interconnectivity. In release 32 there were an average of 3.5 cross-references for each sequence entry.
What is the LISTA database?
the LISTA database of yeast ( Saccharomyces cerevisiae ) genes coding for proteins prepared under the supervisation of Patrick Linder at the University of Geneva ( 4 );
What are the two classes of data in Swiss Prot?
In SWISS-PROT, as in most other sequence databases, 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 a description of the following items: (i) function (s) of the protein; (ii) post-translational modification (s), for example carbohydrates, phosphorylation, acetylation, GPI-anchor, etc.; (iii) domains and sites, for example calcium binding regions, ATP binding sites, zinc fingers, homeobox, kringle, etc.; (iv) secondary structure; (v) quaternary structure; (vi) similarities to other proteins; (vii) disease (s) associated with deficiency of the protein; (viii) sequence conflicts, variants, etc.
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