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.It is a curated protein sequence database, which strives to provide a . Front Genet. 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: Post-translational modification(s). ), a minimal level of redundancy and high level of integration with other databases. RuleBase ( 5 ) manages and stores more than 500 annotation rules, which are applied to defined protein groups in TrEMBL. Species with protein sequences stored in the SWISS-PROT protein database are named according to SWISS-PROT nomenclature: following SWISS-PROT conventions, a systematic approach for naming viral and bacterial strains has been adopted and we endeavor to include both the teleomorph name and the anamorph name for fungi. Annotation added by these methods is checked for relevance and likelihood to a particular sequence. Proc Int Conf Intell Syst Mol Biol. Annotation of all known post-translational modifications in human proteins. Fracture strength and bonding interface morphology of CAD/CAM-fabricated ceramic laminate veneers on bleached enamel treated with two different antioxidants. The last subsection consists of CDS translations where we have strong evidence to believe that these CDS are not coding for real proteins. Some of these files have been available for a long time (the user manual, release notes, the various indices for authors, citations, keywords, etc. Release 11 was based on the translation of all 379 000 CDSs in the EMBL Nucleotide Sequence Database release 58. Uniprot < EMBL-EBI Introduction. Downloads - UniProt List of documents available in SWISS-PROT. To submit new sequence data to SWISS-PROT and for all enquiries regarding the submission process contact: SWISS-PROT, The EMBL OutstationThe European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. We plan to finish annotating all of the remaining yeast sequences (mainly from chromosomes IV, XII, XV and XVI) in early 1997. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. and Wasserman,W.W. For many years, this interconnectivity was achieved almost exclusively via SWISS-PROT DR (Database Cross-Reference) lines, i.e. We believe that the systematic recourse both to publications other than those reporting the core data and to subject referees represents a unique and beneficial feature of SWISS-PROT. 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). Currently, it is often difficult for database users to recognise where individual data items come from. In release 38, there is an average of 4.5 cross-references for each sequence entry. Nucleic Acids Res. Telephone: (+44 1223) 494 400; Telefax : (+44 1223) 494 468; Email: datalib@ebi.ac.uk. (iv) Provide specific indices or documents. for tissues, plasmids and keywords, which are listed in documents distributed with SWISS-PROT (see http://www.expasy.org/sprot/sp-docu.html ). The most efficient and user-friendly way to browse interactively in SWISS-PROT or TrEMBL is to use the ExPASy web server at http://www.expasy.org/ (see http://www.expasy.org/doc/expasy.pdf ), one of its complete and up-to-date mirror sites in Australia, Canada, China, Korea, Taiwan and the USA, or the EBI server ( http://www.ebi.ac.uk/ ). Swiss-Shop requests can be submitted at http://www.expasy. Medically relevant keywords are created continuously and information relevant to the use of specific proteins as therapeutic agents is stored. The remaining 260 000 sequence entries have been automatically merged whenever possible to reduce redundancy in TrEMBL. Bethesda, MD 20894, Web Policies The introduction of TrEMBL as a supplementary database ensured the comprehensiveness of SWISS-PROT and TrEMBL but introduced some degree of redundancy. [PDF] High-quality Protein Knowledge Resource: SWISS-PROT and TrEMBL The extensive integration of SWISS-PROT with specialized databases enables users to navigate through the current knowledge in the Life Sciences providing an insight into the universe of proteins. 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. ), a minimal level of redundancy and a high level of integration with other databases. integrin bond under mechanical load by generating an ideal bond. (, Rebhan,M., Chalifa-Caspi,V., Prilusky,J. The organisms currently selected are: Arabidopsis thaliana (mouse-ear cress), Bacillus subtilis, Caenorhabditis elegans (worm), Candida albicans, Dictyostelium discoideum (slime mold), Drosophila melanogaster (fruit fly), Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Homo sapiens (human), Methanococcus jannaschii, Mus musculus (mouse), Mycobacterium tuberculosis, Mycoplasma genitalium, Saccharomyces cerevisiae (budding yeast), Salmonella typhimurium, Schizosaccharomyces pombe (fission yeast), Sulfolobus solfataricus and Synechocystis sp. We initiated a process to convert the data into mixed case. SWISS-PROT ( 1 ) is a protein sequence and knowledge database that is valued for its high quality annotation, the usage of standardized nomenclature, direct links to specialized databases and minimal redundancy. UniProtKB/Swiss-Prot is now the reviewed section of the UniProt Knowledgebase. The .gov means its official. Antibodies Associated With Autoimmune Encephalitis in Patients With Presumed Neurodegenerative Dementia. (, Wheeler,D.L., Church,D.M., Lash,A.E., Leipe,D.D., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Tatusova,T.A., Wagner,L. The family rules can take into account special conditions required for the proper annotation of these proteins in their specific context. For example calcium binding regions, ATP-binding sites, zinc fingers, homeoboxes, SH2 and SH3 domains, etc. We also make use of the ENZYME database (6), using the EC number as a reference point, to generate standardized description lines for enzyme entries and to allow information such as catalytic activity, cofactors and relevant keywords to be taken from ENZYME and to be added automatically to SP-TrEMBL entries. upd_seq.dat Contains the entries for which the sequence data has been updated since the last release. (, Dunham,I., Shimizu,N., Roe,B.A., Chissoe,S., Hunt,A.R., Collins,J.E., Bruskiewich,R., Beare,D.M., Clamp,M., Smink,L.J. The UniProtKB/Swiss-Prot protein knowledge-base is a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and high level of integration with other databases. IPI ( http://www.ebi.ac.uk/IPI ) provides a top-level guide to the main databases that describe the human proteome, namely SWISS-PROT, TrEMBL, RefSeq and Ensembl. It may be accessed through its Uniform Resource Locator (URL - the addressing system defined in WWW), which is: http://expasy.hcuge.ch/. National Library of Medicine In addition to our efforts in the priority annotation of human proteins (see HPI project) and microbes (see HAMAP), 9 eukaryotic species that are the target of genome sequencing and/or mapping projects are considered as model organisms: Arabidopsis thaliana , Caenorhabditis elegans , Candida albicans , Danio rerio , Dictyostelium discoideum , Drosophila melanogaster , Mus musculus , Saccharomyces cerevisiae and Schizosaccharaomyces pombe . Five complete proteomes have been fully annotated in SWISS-PROT: Escherichia coli , Buchnera aphidicola subsp . nih.gov/Taxonomy/. The creation of additional rules will be one of the priorities for TrEMBL over the next year. and Bork,P. 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. For each species, NEWT displays the SWISS-PROT scientific name, SWISS-PROT common name and SWISS-PROT synonym(s), lineage, number of protein sequence entries in SWISS-PROT and TrEMBL as well as links to each entry. Disease(s) associated with deficiencie(s) in the protein. SP-TrEMBL is partially redundant against SWISS-PROT, since 40 000 of these entries are only additional sequence reports of proteins already in SWISS-PROT. We have recently added cross-references that link SWISS-PROT to the following databases: (i) the Harefield Hospital 2D gel protein databases (4) prepared under the supervisation of Mike Dunn; and (ii) the Maize genome 2D Electrophoresis database (MAIZE-2DPAGE). sharing sensitive information, make sure youre on a federal ), a minimal level of redundancy and high level of integration with othe Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to two additional databases; a variety of new documentation files and the creation of TrEMBL, a computer annotated supplement to SWISS-PROT. *To whom correspondence should be addressed. 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- HHS Vulnerability Disclosure, Help {"type":"entrez-protein","attrs":{"text":"P29965","term_id":"231718"}}, Stoesser G., Tuli,M.A., Lopez,R. In SWISS-PROT, as in most other sequence databases, two classes of data can be distinguished: the core data and the annotation. O'Donovan,C., Martin,M.J., Gattiker,A., Gasteiger,E., Bairoch,A. Federal government websites often end in .gov or .mil. We have initiated the PPAP. We therefore appeal to the user community to fully participate in this initiative by providing all the necessary information to help and to speed up the comprehensive annotation of the human proteome. This should lead to a drastic increase in coverage by automatic annotation. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). The organisms currently selected are: Arabidopsis thaliana (mouse-ear cress), Bacillus subtilis, Caenorhabditis elegans (worm), Candida albicans, Dictyostelium discoideum (slime mold), Drosophila melanogaster (fruit fly), Escherichia coli, Haemophilus influenzae, Homo sapiens (human), Mycobacterium tuberculosis, Mycoplasma genitalium, Saccharomyces cerevisiae (budding yeast), Salmonella typhimurium, Schizosaccharomyces pombe (fission yeast) and Sulfolobus solfataricus (Table 1). Coordinates software development in the SWISS-PROT group at the SIB and is in charge of the ExPASy server. Up-to-date statistics are available at http://www.expasy.org/sprot/relnotes/relstat.html . The site is secure. A special effort is being made to annotate proteins encoded on chromosomes 20, 21 and 22, which were the first chromosomes to be fully sequenced and partially annotated ( 13 15 ). SWISS-PROT is distributed with a large number of documentation files. Please see ftp://ftp.ebi.ac.uk/pub/databases/trembl/evidenceDocumentation.html for more information. Each IPI entry consists of a cluster of related entries from the constituent databases, together with a sequence and a description line taken from a master entry. For TrEMBL to act as a computer-annotated supplement to SWISS-PROT, new procedures have been introduced to remove redundancy (4) and to automatically add highly reliable annotation (5). Data stored in SWISS-PROT used to be represented exclusively in upper case. For a detailed description of the HPI project and its current status please consult http://www.expasy.ch/sprot/hpi/. The tool VARSPLIC ( 3 ), which is freely available ( ftp://ftp.expasy.org/databases/sp_tr_nrdb/varsplic.txt ), enables the recreation of all annotated splice variants from the feature table of a SWISS-PROT entry, or for the complete database. Together with its automatically annotated supplement TrEMBL, it provides a comprehensive and high-quality view of the current state of knowledge about proteins. More recently, implicit links [to currently 22 databases] have been introduced ( 20 ), i.e. PDF The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999 8600 Rockville Pike SUMMARY One of the distinguishing criteria of the SWISS-PROT protein sequence data bank is minimal redundancy. and Apweiler,R. We add and update the annotation of PTMs according to experimental evidence. ), a minimal level of redundancy and a high level of integration with other databases. government site. We will broaden our scope to other species when additional plant genomes become available. The CD-ROMs also contain some database query and retrieval software for MS-DOS and Apple Macintosh computers. Even when all potential coding regions have been predicted, the user community will have at its disposition the sequences of between 80 000 and 100 000 naked proteins. M. Michael Gromiha, in Protein Bioinformatics, 2010. TrEMBL, in particular, contains data automatically imported from the underlying EMBL/DDBJ/GenBank coding sequences, partial manual curation, data imported from other databases, data from specific programs and the results of automatic annotation systems. upd_ann.dat Contains the entries for which one or more annotation fields have been updated since the last release. Before It also contains protein sequences extracted from the literature and protein sequences submitted directly by the user community. Stable identifiers (with incremental versioning) are maintained within IPI facilitating the tracking of sequences between IPI releases. SWISS-PROT, a curated protein sequence data bank, contains not only sequence data but also annotation relevant to a particular sequence. To address this, we introduced TrEMBL (translation of EMBL nucleotide sequence database) in 1996. 1997. The NEWT database ( http://www.ebi.ac.uk/newt/ ) serves as a taxonomic portal to SWISS-PROT and TrEMBL. et al. ), a minimal level of redundancy and high level of integration with To acquire a maximum of up-to-date knowledge regarding a protein, information is not only obtained from publications reporting new sequence data, but also from review articles with an aim to revise periodically the annotations of families or groups of proteins. 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. The ExPASy server was made available to the public in September 1993. If further information on the protein is available, the entries contain detailed annotation on items such as the function(s) of the protein, enzyme-specific information (catalytic activity, cofactors, metabolic pathway, regulation mechanisms), biologically relevant domains and sites, posttranslational modification(s), molecular weight determined by mass spectrometry, subcellular location(s) of the protein, tissue-specific expression, developmentally-specific expression of the protein, secondary structure, quaternary structure, splice isoform(s), polymorphism(s), similarities to other proteins, use of the protein in a biotechnological process, diseases associated with deficiencies in the protein, use of the protein as a pharmaceutical drug, sequence conflicts, etc. SWISS-PROT contains currently 8831 sequence entries from plants, of which 1675 are from A. thaliana. Currently, SWISS-PROT is linked to 31 different databases and has consolidated its role as the major focal point of bio-molecular databases interconnectivity. The SP-TrEMBL and REM-TrEMBL data files require 1.2Gb and 82Mb of disk storage space, respectively. (, O'Donovan,C., Martin,M.J., Glemet,E., Codani,J.-J. There are currently slightly more than 5400 annotated human sequences in SWISS-PROT. Xin J, Chai Z, Zhang C, Zhang Q, Zhu Y, Cao H, Yangji C, Chen X, Jiang H, Zhong J, Ji Q. BMC Genomics. The SWISS-PROT protein sequence database and its supplement TrEMBL in The taxonomic classification used in SWISS-PROT is that maintained at the NCBI (see http://www.ncbi.nlm.nih.gov/Taxonomy/ ). Right from the start, SWISS-PROT aimed to standardize the nomenclature for a given protein and its isoforms across related organisms. and Douglas,S.A. We stopped entering immunoglobulins and T-cell receptors into SWISS-PROT, because we only want to keep the germ line gene derived translations of these proteins in SWISS-PROT and not all known somatic recombinated variations of these proteins. (, Hattori,M., Fujiyama,A., Taylor,T.D., Watanabe,H., Yada,T., Park,H.S., Toyoda,A., Ishii,K., Totoki,Y., Choi,D.K. Consistent nomenclature is indispensable for communication and literature search. A sample SWISS-PROT entry is shown in http://www.expasy.ch/cgi-bin/niceprot. Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL. Another category of data which will not be included in SWISS-PROT are synthetic sequences. (, Wain,H.M., Lush,M., Ducluzeau,F. Evidence tags will allow users to trace the source of each data item added by a curator and to readily distinguish between experimental and predicted data. SWISS-PROT + TREMBL - PubMed Your comment will be reviewed and published at the journal's discretion. Disclaimer. 1) The UniProt Knowledgebase (UniProtKB) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The data file (sequences and annotations) requires 377Mb of disk storage space. Yu Z, Ding Y, Yin J, Yu D, Zhang J, Zhang M, Ding M, Zhong W, Qiu J, Li J. Int J Mol Sci. Plant Physiol Biochem. 2022 Nov 4;23(21):13546. doi: 10.3390/ijms232113546. [PDF] Removing Redundancy in SWISS-PROT and TrEMBL - Semantic Scholar Right now this process affects only 15% of all TrEMBL entries. With exemplary model organisms in view, we accomplished high annotation standards that were transferred to all the database entries. Cross-references to these databases are regularly updated. Annotation of mammalian orthologs of human proteins. TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries, which are not yet integrated in SWISS-PROT. New Developments in Linking of Biological Databases and Computer Brand names, as well as names of companies developing and selling the drug are also indicated. Inclusion in an NLM database does not imply endorsement of, or agreement with, The Swiss Institute of Bioinformatics (SIB) and the EMBL/EBI mandated the company Geneva Bioinformatics (GeneBio) (see http://www.genebio.com ) to act as their representative for the purpose of concluding the necessary license agreements and levying the fees. Differences between sequencing reports due to splice variants, polymorphisms, disease-causing mutations, experimental sequence modifications or simply sequencing errors are indicated in the feature table of the corresponding SWISS-PROT entry. Up-to-date statistics are available at http://www.expasy.org/sprot/hpi/hpi_stat.html . The complexity due to all these modifications is compounded by the high level of diversity that alternative splicing can produce at the level of sequence. During the next 9 months a major effort will be made to supplement the already quite comprehensive description of known post-translational modifications in human proteins currently provided in 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.
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