1473:
633:
redundancy, UniParc stores each unique sequence only once. Identical sequences are merged, regardless of whether they are from the same or different species. Each sequence is given a stable and unique identifier (UPI), making it possible to identify the same protein from different source databases. UniParc contains only protein sequences, with no annotation. Database cross-references in UniParc entries allow further information about the protein to be retrieved from the source databases. When sequences in the source databases change, these changes are tracked by UniParc and history of all changes is archived.
2187:
45:
2199:
472:-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.
599:
UniProtKB/TrEMBL contains high-quality computationally analyzed records, which are enriched with automatic annotation. It was introduced in response to increased dataflow resulting from genome projects, as the time- and labour-consuming manual annotation process of UniProtKB/Swiss-Prot could not be
459:
UniProt
Knowledgebase (UniProtKB) is a protein database partially curated by experts, consisting of two sections: UniProtKB/Swiss-Prot (containing reviewed, manually annotated entries) and UniProtKB/TrEMBL (containing unreviewed, automatically annotated entries). As of 22 February 2023,
435:
and high level of integration with other databases. Recognizing that sequence data were being generated at a pace exceeding Swiss-Prot's ability to keep up, TrEMBL (Translated EMBL Nucleotide
Sequence Data Library) was created to provide automated annotations for those proteins not in Swiss-Prot.
632:
UniProt
Archive (UniParc) is a comprehensive and non-redundant database, which contains all the protein sequences from the main, publicly available protein sequence databases. Proteins may exist in several different source databases, and in multiple copies in the same database. In order to avoid
387:(Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. 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,
2042:
503:, unidentified conflicts). A range of sequence analysis tools is used in the annotation of UniProtKB/Swiss-Prot entries. Computer-predictions are manually evaluated, and relevant results selected for inclusion in the entry. These predictions include post-translational modifications,
399:
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 (PIR-PSD). These databases coexisted with differing
460:
release "2023_01" of UniProtKB/Swiss-Prot contains 569,213 sequence entries (comprising 205,728,242 amino acids abstracted from 291,046 references) and release "2023_01" of UniProtKB/TrEMBL contains 245,871,724 sequence entries (comprising 85,739,380,194 amino acids).
776:
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.
763:
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
1329:
Apweiler, R.; Bairoch, A.; Wu, C. H.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M. J.; Natale, D. A.; o’Donovan, C.; Redaschi, N.; Yeh, L. S. (2004).
351:. 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
1987:
1951:
1890:
1785:
1969:
959:
Wu, C. H.; Yeh, L. S.; Huang, H.; Arminski, L.; Castro-Alvear, J.; Chen, Y.; Hu, Z.; Kourtesis, P.; Ledley, R. S.; Suzek, B. E.; Vinayaka, C. R.; Zhang, J.; Barker, W. C. (2003).
1008:
Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M. C.; Estreicher, A.; Gasteiger, E.; Martin, M. J.; Michoud, K.; O'Donovan, C.; Phan, I.; Pilbout, S.; Schneider, M. (2003).
526:. The full text of each paper is read, and information is extracted and added to the entry. Annotation arising from the scientific literature includes, but is not limited to:
2240:
1981:
1420:
2048:
1995:
1896:
423:. Swiss-Prot aimed to provide reliable protein sequences associated with a high level of annotation (such as the description of the function of a protein, its
2024:
2059:
2036:
772:
of all the merged entries and links to the corresponding UniProtKB and UniParc records are displayed. UniRef100 sequences are clustered using the CD-HIT
468:
UniProtKB/Swiss-Prot is a manually annotated, non-redundant protein sequence database. It combines information extracted from scientific literature and
2030:
746:
1617:
793:
2245:
2018:
1795:
591:
Annotated entries undergo quality assurance before inclusion into UniProtKB/Swiss-Prot. When new data becomes available, entries are updated.
1975:
1873:
1518:
Suzek, B. E.; Huang, H.; McGarvey, P.; Mazumder, R.; Wu, C. H. (2007). "UniRef: Comprehensive and non-redundant UniProt reference clusters".
1731:
726:
391:'s Atlas of Protein Sequence and Structure, first published in 1965. In 2002, EBI, SIB, and PIR joined forces as the UniProt consortium.
2001:
1107:
919:
1553:
Li, W.; Jaroszewski, L.; Godzik, A. (2001). "Clustering of highly homologous sequences to reduce the size of large protein databases".
2053:
1957:
1924:
1907:
1867:
769:
420:
412:
383:
in
Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the
372:
368:
118:
114:
1855:
1843:
1685:
483:
are merged into the same database entry. Differences between sequences are identified, and their cause documented (for example
428:
2255:
1902:
157:
888:
1822:
1739:
1707:
797:
720:
1503:
1412:
2152:
1671:
1610:
697:
380:
376:
122:
451:
UniProt provides four core databases: UniProtKB (with sub-parts Swiss-Prot and TrEMBL), UniParc, UniRef and
Proteome.
324:
Yes – manual and automatic. Rules for automatic annotation generated by database curators and computational algorithms.
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1703:
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685:
558:
234:
2225:
1760:
2230:
2203:
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709:
348:
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The consortium members pooled their overlapping resources and expertise, and launched UniProt in
December 2003.
1913:
573:
553:
2250:
2191:
2157:
1800:
1653:
1603:
1381:
1296:
600:
broadened to include all available protein sequences. The translations of annotated coding sequences in the
544:
388:
604:
are automatically processed and entered in UniProtKB/TrEMBL. UniProtKB/TrEMBL also contains sequences from
2121:
1861:
1649:
667:
492:
153:
2142:
1755:
617:
271:
781:
2126:
1108:"Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!"
504:
484:
1443:
2235:
2116:
2043:
International
Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
1935:
1723:
801:
691:
500:
301:
2172:
2076:
1879:
674:
FlyBase: the primary repository of genetic and molecular data for the insect family
Drosophilidae
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437:
2167:
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1363:
1248:
1196:
1157:
1129:
1088:
1039:
990:
941:
855:
703:
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Currently UniParc contains protein sequences from the following publicly available databases:
605:
508:
488:
918:
O'Donovan, C.; Martin, M. J.; Gattiker, A.; Gasteiger, E.; Bairoch, A.; Apweiler, R. (2002).
2147:
2111:
1919:
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401:
344:
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288:
732:
1838:
432:
265:
109:
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1442:
Leinonen, R.; Diez, F. G.; Binns, D.; Fleischmann, W.; Lopez, R.; Apweiler, R. (2004).
1243:
1218:
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679:
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424:
356:
352:
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Microsoft Research - University of Trento Centre for Computational and Systems Biology
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1058:
1034:
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2101:
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804:, the Swiss Federal Government through the Federal Office of Education and Science,
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227:
143:
1192:
44:
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2096:
1715:
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469:
743:
UniProtKB/Swiss-Prot, UniProtKB/Swiss-Prot protein isoforms, UniProtKB/TrEMBL
773:
768:) into a single UniRef entry. The sequence of a representative protein, the
621:
540:
242:
1574:
1539:
1469:
1367:
1252:
1200:
1179:
Apweiler, R.; Bairoch, A.; Wu, C. H. (2004). "Protein sequence databases".
1133:
1043:
994:
945:
859:
1092:
1074:
936:
17:
1790:
1727:
1719:
1689:
1348:
1234:
1059:"The SWISS-PROT protein sequence data bank and its new supplement TREMBL"
1025:
976:
841:
765:
752:
94:
76:
1010:"The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003"
1765:
1711:
1641:
673:
662:
656:
609:
480:
436:
Meanwhile, PIR maintained the PIR-PSD and related databases, including
275:
72:
1963:
1817:
1770:
1735:
715:
613:
536:
523:
384:
31:
1490:
522:
Relevant publications are identified by searching databases such as
203:
1849:
1775:
1148:
Naissance d’une banque de données: Interview du prof. Amos Bairoch
805:
645:
601:
149:
1595:
1389:
1304:
1693:
920:"High-quality protein knowledge resource: SWISS-PROT and TrEMBL"
652:
648:
620:. Since 22 July 2021 it also includes structures predicted with
496:
476:
252:
247:
1599:
183:
569:
237:
161:
1152:
877:. Silver Spring, Md: National Biomedical Research Foundation.
579:
Protein variant forms produced by natural genetic variation,
75:
data created by combining the Swiss-Prot, TrEMBL and PIR-PSD
1952:
African Society for Bioinformatics and Computational Biology
347:
and functional information, many entries being derived from
1891:
Max Planck Institute of Molecular Cell Biology and Genetics
1590:
215:
173:
1970:
International Nucleotide Sequence Database Collaboration
440:, a database of protein sequences and curated families.
27:
Database of protein sequences and functional information
1413:"Putting the power of AlphaFold into the world's hands"
1382:"Where do the UniProtKB protein sequences come from?"
566:
Locations and roles of significant domains and sites
2135:
2069:
2011:
1944:
1831:
1809:
1748:
1633:
889:"2002 Release: NHGRI Funds Global Protein Database"
602:
EMBL-Bank/GenBank/DDBJ nucleotide sequence database
328:
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264:
259:
226:
198:
168:
142:
137:
129:
108:
103:
93:
83:
56:
51:
1662:, database of protein sequences grouping together
1219:"The Universal Protein Resource (UniProt) in 2010"
334:Yes – both individual protein entries and searches
1267:"UniProtKB/Swiss-Prot Release 2023_01 statistics"
1897:US National Center for Biotechnology Information
1297:"How do we manually annotate a UniProtKB entry?"
893:National Human Genome Research Institute (NHGRI)
1982:International Society for Computational Biology
1513:
1511:
1324:
1322:
1212:
1210:
1174:
1172:
1170:
587:processing, and post-translational modification
2049:ISCB Africa ASBCB Conference on Bioinformatics
1504:ftp://ftp.isrec.isb-sib.ch/pub/databases/trome
1332:"UniProt: The Universal Protein knowledgebase"
1996:Institute of Genomics and Integrative Biology
1611:
8:
2025:European Conference on Computational Biology
37:
2060:Research in Computational Molecular Biology
1663:
2037:International Conference on Bioinformatics
1618:
1604:
1596:
36:
2031:Intelligent Systems for Molecular Biology
1459:
1357:
1347:
1242:
1123:
1082:
1033:
984:
935:
849:
747:Vertebrate and Genome Annotation Database
213:& for downloading complete data sets
2241:Science and technology in Cambridgeshire
1291:
1289:
1287:
826:"UniProt: a hub for protein information"
794:National Human Genome Research Institute
2019:Basel Computational Biology Conference
1667:
875:Atlas of protein sequence and structure
816:
608:, and from gene prediction, including
431:, variants, etc.), a minimal level of
278:O, bulk retrieval/download, ID mapping
71:ein resource, a central repository of
1976:International Society for Biocuration
1874:European Molecular Biology Laboratory
824:UniProt, Consortium. (January 2015).
792:UniProt is funded by grants from the
447:Organization of the UniProt databases
367:The UniProt consortium comprises the
7:
2198:
1388:. September 21, 2011. Archived from
1303:. September 21, 2011. Archived from
808:, and the US Department of Defense.
727:The Arabidopsis Information Resource
411:during his PhD and developed by the
404:coverage and annotation priorities.
355:organisations and a foundation from
2002:Japanese Society for Bioinformatics
1181:Current Opinion in Chemical Biology
343:is a freely accessible database of
1964:European Molecular Biology network
1479:from the original on Mar 30, 2024.
1057:Bairoch, A.; Apweiler, R. (1996).
961:"The Protein Information Resource"
407:Swiss-Prot was created in 1986 by
395:The roots of the UniProt databases
25:
2054:Pacific Symposium on Biocomputing
1958:Australia Bioinformatics Resource
1925:Swiss Institute of Bioinformatics
1908:Netherlands Bioinformatics Centre
1868:European Bioinformatics Institute
1423:from the original on 24 July 2021
421:European Bioinformatics Institute
413:Swiss Institute of Bioinformatics
373:Swiss Institute of Bioinformatics
369:European Bioinformatics Institute
2197:
2186:
2185:
1856:Database Center for Life Science
1844:Computational Biology Department
1732:Arabidopsis Information Resource
1411:Hassabis, Demis (22 July 2022).
429:post-translational modifications
43:
1702:Specialised genomic databases:
1567:10.1093/bioinformatics/17.3.282
1903:Japanese Institute of Genetics
1125:10.1093/bioinformatics/16.1.48
539:-specific information such as
415:and subsequently developed by
1:
2246:South Cambridgeshire District
1823:Rosalind (education platform)
1740:Zebrafish Information Network
1708:Saccharomyces Genome Database
1532:10.1093/bioinformatics/btm098
1491:"Protein Research Foundation"
1461:10.1093/bioinformatics/bth191
1229:(Database issue): D142–D148.
873:Dayhoff, Margaret O. (1965).
798:National Institutes of Health
780:UniRef is available from the
721:Saccharomyces Genome Database
659:nucleotide sequence databases
515:, domain identification, and
2153:List of biological databases
1672:Protein Information Resource
698:Protein Information Resource
576:- and cofactor-binding sites
559:Protein-protein interactions
381:Wellcome Trust Genome Campus
377:Protein Information Resource
1646:European Nucleotide Archive
924:Briefings in Bioinformatics
836:(Database issue): D204–12.
710:Protein Research Foundation
686:International Protein Index
379:(PIR). EBI, located at the
2272:
1193:10.1016/j.cbpa.2003.12.004
349:genome sequencing projects
29:
2181:
1931:Wellcome Sanger Institute
1885:J. Craig Venter Institute
42:
1914:Philippine Genome Center
583:, alternative splicing,
475:Sequences from the same
30:Not to be confused with
2158:Molecular phylogenetics
1654:China National GeneBank
680:H-Invitational Database
1862:DNA Data Bank of Japan
1650:DNA Data Bank of Japan
1336:Nucleic Acids Research
1223:Nucleic Acids Research
1063:Nucleic Acids Research
1014:Nucleic Acids Research
965:Nucleic Acids Research
830:Nucleic Acids Research
668:European Patent Office
530:Protein and gene names
363:The UniProt consortium
2256:Computational biology
2143:Computational biology
1658:Secondary databases:
563:Pattern of expression
505:transmembrane domains
1640:Sequence databases:
1342:(90001): 115D–1119.
1217:Uniprot, C. (2009).
1146:Séverine Altairac, "
1106:Bairoch, A. (2000).
899:on 24 September 2015
554:Subcellular location
485:alternative splicing
464:UniProtKB/Swiss-Prot
296:Attribution-NoDerivs
1936:Whitehead Institute
1724:Rat Genome Database
1075:10.1093/nar/24.1.21
937:10.1093/bib/3.3.275
802:European Commission
692:Japan Patent Office
39:
2173:Sequence alignment
1880:Flatiron Institute
1349:10.1093/nar/gkh131
1235:10.1093/nar/gkp846
1153:Protéines à la Une
1026:10.1093/nar/gkg095
977:10.1093/nar/gkg040
842:10.1093/nar/gku989
549:catalytic residues
541:catalytic activity
148:Custom flat file,
133:UniProt Consortium
89:Protein annotation
2226:Protein databases
2213:
2212:
2168:Sequence database
1682:Protein Data Bank
1676:Other databases:
1526:(10): 1282–1288.
1454:(17): 3236–3237.
1444:"UniProt archive"
770:accession numbers
704:Protein Data Bank
495:sites, incorrect
489:natural variation
338:
337:
270:Advanced search,
16:(Redirected from
2263:
2231:Online databases
2201:
2200:
2189:
2188:
2148:List of biobanks
2112:Stockholm format
1920:Scripps Research
1620:
1613:
1606:
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904:
895:. Archived from
885:
879:
878:
870:
864:
863:
853:
821:
782:UniProt FTP site
738:US Patent Office
637:Source databases
595:UniProtKB/TrEMBL
519:classification.
402:protein sequence
389:Margaret Dayhoff
345:protein sequence
294:Creative Commons
255:
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222:
219:
217:
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130:Primary citation
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2007:
1988:Student Council
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1839:Broad Institute
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1805:
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1392:on Dec 15, 2013
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1307:on Dec 13, 2013
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513:signal peptides
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375:(SIB), and the
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321:Curation policy
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121:, Switzerland;
110:Research center
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2136:Related topics
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1585:External links
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1561:(3): 282–283.
1555:Bioinformatics
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1448:Bioinformatics
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1271:web.expasy.org
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1112:Bioinformatics
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531:
517:protein family
465:
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357:Washington, DC
353:bioinformatics
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2102:Pileup format
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1945:Organizations
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1698:Gene Ontology
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494:
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479:and the same
478:
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454:
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426:
422:
418:
417:Rolf Apweiler
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286:
283:Miscellaneous
281:
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136:
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98:
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82:
78:
74:
70:
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62:
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50:
46:
41:
33:
19:
2202:
2190:
2097:Nexus format
2092:NeXML format
2087:FASTQ format
2082:FASTA format
2070:File formats
1832:Institutions
1659:
1558:
1554:
1548:
1523:
1519:
1499:
1485:
1451:
1447:
1437:
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1416:
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897:the original
892:
883:
874:
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779:
762:
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598:
590:
521:
499:boundaries,
491:, incorrect
474:
467:
458:
450:
442:
409:Amos Bairoch
406:
398:
366:
340:
339:
329:Bookmarkable
311:Data release
199:Download URL
68:
64:
60:
2077:CRAM format
1998:(CSIR-IGIB)
800:(NIH), the
585:proteolytic
581:RNA editing
501:frameshifts
427:structure,
371:(EBI), the
228:Web service
144:Data format
57:Description
2236:Proteomics
2220:Categories
2163:Sequencing
2127:GTF format
2122:GFF format
2117:VCF format
2107:SAM format
1870:(EMBL-EBI)
1796:SOAP suite
1716:VectorBase
1678:BioNumbers
1664:Swiss-Prot
812:References
622:AlphaFold2
493:initiation
470:biocurator
433:redundancy
302:Versioning
210:/downloads
84:Data types
18:Swiss-Prot
1990:(ISCB-SC)
1960:(EMBL-AR)
1893:(MPI-CBG)
1634:Databases
1162:1660-9824
806:NCI-caBIG
774:algorithm
700:(PIR-PSD)
676:(FlyBase)
574:substrate
545:cofactors
455:UniProtKB
438:iProClass
313:frequency
250:see info
240:see info
95:Organisms
77:databases
2192:Category
2062:(RECOMB)
2012:Meetings
1966:(EMBnet)
1816:Server:
1791:SAMtools
1786:PANGOLIN
1749:Software
1728:PHI-base
1720:WormBase
1690:InterPro
1575:11294794
1540:17379688
1474:Archived
1470:15044231
1421:Archived
1417:Deepmind
1396:14 April
1368:14681372
1311:14 April
1276:31 March
1253:19843607
1201:15036160
1134:10812477
1044:12520024
995:12520019
946:12230036
903:14 April
860:25348405
766:organism
753:WormBase
533:Function
509:topology
331:entities
218:.uniprot
206:.uniprot
186:.uniprot
176:.uniprot
115:EMBL-EBI
86:captured
2204:Commons
2039:(InCoB)
1984:(ISCB)
1972:(INSDC)
1954:(ASBCB)
1858:(DBCLS)
1852:(COSBI)
1766:Clustal
1712:FlyBase
1686:Ensembl
1660:UniProt
1642:GenBank
1591:UniProt
1427:24 July
1386:UniProt
1301:UniProt
1244:2808944
1093:8594581
851:4384041
788:Funding
740:(USPTO)
682:(H-Inv)
663:Ensembl
657:GenBank
628:UniParc
610:Ensembl
481:species
419:at the
359:, USA.
341:UniProt
316:8 weeks
289:License
276:Clustal
169:Website
104:Contact
73:protein
67:versal
63:is the
61:UniProt
52:Content
38:UniProt
2045:(CIBB)
2033:(ISMB)
2027:(ECCB)
2004:(JSBi)
1910:(NBIC)
1899:(NCBI)
1887:(JCVI)
1876:(EMBL)
1864:(DDBJ)
1818:ExPASy
1801:TopHat
1781:MUSCLE
1771:EMBOSS
1761:Bowtie
1736:GISAID
1696:, and
1668:TrEMBL
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796:, the
759:UniRef
749:(VEGA)
729:(TAIR)
716:RefSeq
651:-Bank/
614:RefSeq
537:Enzyme
524:PubMed
425:domain
385:ExPASy
246:&
233:Yes –
138:Access
117:, UK;
32:UniPro
2056:(PSB)
1978:(ISB)
1927:(SIB)
1916:(PGC)
1846:(CBD)
1810:Other
1776:HMMER
1756:BLAST
1477:(PDF)
733:TROME
723:(SGD)
712:(PRF)
706:(PDB)
694:(JPO)
688:(IPI)
670:(EPO)
646:INSDC
272:BLAST
260:Tools
190:/news
150:FASTA
125:, US.
1738:and
1704:BOLD
1694:KEGG
1670:and
1652:and
1571:PMID
1536:PMID
1466:PMID
1429:2021
1398:2018
1364:PMID
1313:2018
1278:2023
1249:PMID
1197:PMID
1158:ISSN
1130:PMID
1089:PMID
1040:PMID
991:PMID
942:PMID
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856:PMID
653:DDBJ
649:EMBL
618:CCDS
616:and
547:and
507:and
497:exon
477:gene
253:here
248:REST
243:here
235:JAVA
220:.org
208:.org
188:.org
178:.org
69:Prot
1563:doi
1528:doi
1456:doi
1354:PMC
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1120:doi
1079:PMC
1071:doi
1030:PMC
1022:doi
981:PMC
973:doi
932:doi
846:PMC
838:doi
606:PDB
572:-,
570:Ion
306:Yes
266:Web
238:API
230:URL
216:ftp
204:www
184:www
174:www
162:XML
158:RDF
154:GFF
123:PIR
119:SIB
99:All
65:Uni
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
