[email protected] group, GenevaSIB Swiss Institute of Bioinformatics
The UniProt knowledgebase
www.uniprot.org
a hub of integrated protein data
Science cover, february 2011
protein sequence functional information data knowledge
UniProt consortium
EBI : European Bioinformatics Institute (UK)SIB : Swiss Institute of Bioinformatics (CH)PIR : Protein information resource (US)
www.uniprot.org
UniProt databases
UniProtKB: protein sequence knowledgebase, 2 sections UniProtKB/Swiss-Prot and UniProtKB/TrEMBL (query, Blast, download) (~15 mo entries)
UniParc: protein sequence archive (ENA equivalent at the
protein level). Each entry contains a protein sequence with cross-links to other databases where you find the sequence (active or not). Not annotated (query, Blast, download) (~25 mo entries)
UniRef: 3 clusters of protein sequences with 100, 90 and 50 % identity; useful to speed up sequence similarity search (BLAST) (query, Blast, download) (UniRef100 10 mo entries; UniRef90 7 mo entries; UniRef50 3.3 mo entries)
UniMES: protein sequences derived from metagenomic projects (mostly Global Ocean Sampling (GOS)) (download) (8 mo entries, included in UniParc)
UniProt databasesThe central piece
UniProtKBan encyclopedia on proteins
composed of 2 sectionsUniProtKB/TrEMBL and UniProtKB/Swiss-Prot
unreviewed and reviewed automatically annotated and manually annotated
released every 4 weeks
UniProtKBOrigin of protein sequences
UniProtKB protein sequences are mainly derived from
- INSDC (translated submitted coding sequences - CDS)- Ensembl (gene prediction ) and RefSeq sequences- Sequences of PDB structures- Direct submission or sequences scanned from literature
Notes: - UniProt is not doing any gene prediction- Most non-germline immunoglobulins, T-cell receptors , most patent
sequences, highly over-represented data (e.g. viral antigens), pseudogenes sequences are excluded from UniProtKB, - but stored in UniParc
- Data from the PIR database have been integrated in UniProtKB since 2003.
15 %
85 %
Swiss-Prot
TrEMBL
EMBL
Automated extraction of protein sequence (translated CDS), gene name and
references.Automated annotation
Manual annotation of the sequence and associated
biological information
UniProtKB/TrEMBL
unreviewedAutomatic annotation
released every 4 weeks
One protein sequenceOne species
Automated annotationKeywords
and Gene Ontology
Automated annotationFunction, Subcellular location,
Catalytic activity, Sequence similarities…
Automated annotationtransmembrane domains,
signal peptide…
Cross-references to over 125 databases
References
Protein and gene namesTaxonomic information
UniProtKB/TrEMBLwww.uniprot.org
UniProtKB/TrEMBL
Automatic annotation Protein sequence
- The quality of the protein sequences is dependent on the information provided by the submitter of the original nucleotide entry (CDS) or of the gene prediction pipeline (i.e. Ensembl). - 100% identical sequences (same length, same organism are merged automatically).
Biological information Sources of annotation- Provided by the submitter (EMBL, PDB, TAIR…)- From automated annotation (automated generated annotation
rules (i.e. SAAS) and/or manually generated annotation rules (i.e. UniRule))
Example of fully automatic annotation: SAAS
• Rules are derived from the UniProtKB/Swiss-Prot manual annotation.
• Fully automated rule generation based on C4.5 decision tree algorithm.
• One annotation, one rule.
• High stringency – require 99% or greater estimated precision to generate annotation (test on UniProtKB/Swiss-Prot)
• Rules are produced, updated and validated at each release.
UniProtKB/TrEMBL
UniProtKB/Swiss-Prot
reviewedmanually annotated
released every 4 weeks
MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG
One protein sequenceOne gene
One species
Manual annotationKeywords
and Gene Ontology
Manual annotationFunction, Subcellular location,
Catalytic activity, Disease, Tissue specificty, Pathway…
Manual annotationPost-translational modifications,
variants, transmembrane domains, signal peptide…
Cross-references to over 125 databases
References
Protein and gene namesTaxonomic information
Alternative products:protein sequences produced by
alternative splicing, alternative promoter usage,
alternative initiation…
UniProtKB/Swiss-Protwww.uniprot.org
UniProtKB/Swiss-Prot
Manual annotation
1. Protein sequence (merge available CDS, annotate sequence discrepancies, report sequencing mistakes…)
2. Biological information (sequence analysis, extract literature information, ortholog data propagation, …)
UniProtKB/Swiss-Prot
1- Protein sequence curation
The displayed protein sequence: …canonical, representative, consensus…
+alternative sequences (described within the entry)
1 entry <-> 1 gene (1 species)
UniProtKB/Swiss-Prot
a gene-centric view of the protein space
What is the current status?• At least 20% of Swiss-Prot entries required a
minimal amount of curation effort so as to obtain the “correct” sequence.
• Typical problems– unsolved conflicts– uncorrected initiation sites– frameshifts– wrong gene prediction– other ‘problems’
UCSC genome browserexamples of CDS annotation submitted to INSDC…
UniProtKB/Swiss-Prot
2- Biological data curation
UniProtKB/Swiss-Prot gathers data form multiple sources:
- publications (literature/Pubmed)- prediction programs (Prosite, TMHMM, …)- contacts with experts - other databases- nomenclature committees
An evidence attribution system allows to easily trace the source of each annotation
Extract literature informationand protein sequence analysis
maximum usage of controlled vocabulary
Protein and gene names
…enable researchers to obtain a summary of what is known about a protein…
General annotation (Comments)
www.uniprot.org
Human protein manual annotation: some statistics (June 2011)
Sequence annotation (Features)
…enable researchers to obtain a summary of what is known about a protein…
www.uniprot.org
Non-experimental qualifiers UniProtKB/Swiss-Prot considers both experimental and
predicted data and makes a clear distinction between both
Type of evidence QualifierStrong experimental evidence None or Ref.X
Light experimental evidence Probable
Inferred by similarity with homologous protein
By similarity
Inferred by prediction Potential
Find all the proteins localized in the cytoplasm (experimentally
proven) which are phosphorylated on a serine
(experimentally proven)
• The ‘Protein existence’ tag indicates what is the evidence for the existence of a given protein;
• Different qualifiers:1. Evidence at protein level (~18%) (MS, western blot (tissue specificity), immuno (subcellular
location),…)2. Evidence at transcript level (~19%)3. Inferred from homology (~58 %)4. Predicted (~5%)5. Uncertain (mainly in TrEMBL)
‘Protein existence’ tag
http://www.uniprot.org/docs/pe_criteria
UniProtKBAdditional information
can be found in the cross-references (to more than 140 databases)
2D gel2DBase-EcoliANU-2DPAGEAarhus/Ghent-2DPAGE (no server)COMPLUYEAST-2DPAGECornea-2DPAGE DOSAC-COBS-2DPAGEECO2DBASE (no server)OGPPHCI-2DPAGEPMMA-2DPAGERat-heart-2DPAGEREPRODUCTION-2DPAGESiena-2DPAGESWISS-2DPAGEUCD-2DPAGEWorld-2DPAGE
Family and domainGene3DHAMAPInterProPANTHERPfamPIRSFPRINTSProDomPROSITESMARTSUPFAMTIGRFAMs
Organism-specificAGDArachnoServerCGDConoServerCTDCYGD dictyBaseEchoBASEEcoGeneeuHCVdbEuPathDBFlyBaseGeneCardsGeneDB_SpombeGeneFarmGenoListGrameneH-InvDB HGNCHPA LegioListLepromaMaizeGDBMGIMIMneXtProtOrphanet PharmGKBPseudoCAPRGDSGDTAIRTubercuListWormBaseXenbaseZFIN
Protein family/groupAllergomeCAZyMEROPSPeroxiBasePptaseDBREBASETCDB
Genome annotationEnsemblEnsemblBacteriaEnsemblFungiEnsemblMetazoaEnsemblPlantsEnsemblProtistsGeneIDGenomeReviewsKEGGNMPDRTIGRUCSCVectorBase
Enzyme and pathwayBioCycBRENDAPathway_Interaction_DBReactome
OtherBindingDBDrugBank NextBio PMAP-CutDB
SequenceEMBLIPIPIRRefSeqUniGene
3D structureDisProtHSSPPDBPDBsumProteinModelPortalSMR
PTMGlycoSuiteDBPhosphoSitePhosSite
UniProtKB/Swiss-Prot:129 explicit links
and 14 implicit links!
ProteomicPeptideAtlasPRIDEProMEX
PPIDIPIntAct MINTSTRING
Phylogenomic dbseggNOGGeneTreeHOGENOMHOVERGENInParanoidOMAOrthoDBPhylomeDBProtClustDB
PolymorphismdbSNP
Gene expressionArrayExpressBgeeCleanExGenevestigatorGermOnline
Ontologies GO
The UniProt web site www.uniprot.org
• Powerful search engine, google-like and easy-to-use, but also supports very directed field searches
• Scoring mechanism presenting relevant matches first
• Entry views, search result views and downloads are customizable
• The URL of a result page reflects the query; all pages and queries are bookmarkable, supporting programmatic access
• Search, Blast, Align, Retrieve, ID mapping
Search
A very powerful text search tool with autocompletion and refinement
options allowing to look for UniProt entries and documentation by
biological information
Find all human proteins located in the nucleus
The search interface guides users with helpful suggestions and hints
Advanced Search
A very powerful search tool
To be used when you know in which entry section the information is stored
Find all the protein localized in the cytoplasm (experimentally
proven) which are phosphorylated on a serine
(experimentally proven)
Result pages: highly customizable
Result pages: downloadable
The URL can be bookmarked and manually
modified.
Blast
A tool associated with the standard options to search
sequences in different UniProt databases and
data sets
Blast: customize the result display
Blast: local alignment sequence annotation highlighting option
Align
A ClustalW multiple alignment tool with
sequence annotation highlighting option
Align
sequence annotation highlighting option
Retrieve
A UniProt specific tool allowing to retrieve a list of entries in several standard identifiers formats.
You can then query your ‘personal database’ with the UniProt search tool.
Query your own dataset
ID Mapping
Gives the possibility to get a mapping between different databases for a given
protein
These identifiers are all pointing to a TP53 (p53) protein sequence !
P04637, NP_000537, NP_001119584.1, NP_001119585.1, NP_001119584.1, NP_001119584.1, NP_001119584.1, NP_001119584.1, ENSG00000141510, CCDS11118, UPI000002ED67, IPI00025087, etc.
Download
Download UniProt http://www.uniprot.org/downloads
Canonical and isoform sequences (fasta format)
A few words on the UniProt ‘complete proteome’
sequence sets…
2’747 complete proteomes
Genome completely sequenced
Proteins mapped to the genome
Entries tagged with the KW ‘Complete proteome’
UniProtKB/Swiss-Prot isoform sequences are available in FASTA format only
Fully manually reviewed (e.g. S. cerevisiae)Partially manually reviewed (e.g. Homo sapiens)Unreviewed (e.g. Acinetobacter baumannii (strain 1656-2))
UniProtKB - complete proteomes
Can be downloaded:
From our complete proteome page www.uniprot.org/taxonomy/complete-proteomes
From the ‘ftp download ‘ page
By querying UniProtKB + download Query: organism:93062 AND keyword:"complete proteome"
UniProtKB - complete proteomes
Additional information: www.uniprot.org/faq/15
Query UniProtKB + download
Human proteome ~ 20’200 genes
Query for ‘homo sapiens’ (August 2011)• UniProtKB: 110,056 entries + alt sequences (~ 15’435) = 125’491• UniProtKB/Swiss-Prot: 20’244 entries + alt sequences (~ 15’435) =
35’679• UniProtKB/TrEMBL: 89,834 entries• RefSeq: 32’898 sequences• Ensembl: 90’720 sequences
Query for ‘homo sapiens’ + Complete proteome (KW-181)• UniProtKB: 56’392 + alt sequences (15’435) = 71’827• UniProtKB/Swiss-Prot: 20’238 + alt sequences (15’435) = 35’673• UniProtKB/TrEMBL: 36’154
92% of human entries are linked with at least one RefSeq entry…
Summary
Do not hesitate to contact us !
The UniProt ConsortiumSIBIoannis Xenarios, Lydie Bougueleret, Andrea Auchincloss, Kristian Axelsen, Delphine Baratin, Marie-Claude Blatter, Brigitte Boeckmann, Jerven Bolleman, Laurent Bollondi, Emmanuel Boutet, Lionel Breuza, Alan Bridge, Edouard de Castro, Lorenzo Cerutti, Elisabeth Coudert, Béatrice Cuche, Mikael Doche, Dolnide Dornevil, Severine Duvaud, Anne Estreicher, Livia Famiglietti, Marc Feuermann, Sebastien Gehant, Elisabeth Gasteiger, Alain Gateau, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nicolas Hulo, Janet James, Florence Jungo, Guillaume Keller, Vicente Lara, Philippe Lemercier, Damien Lieberherr, Xavier Martin, Patrick Masson, Anne Morgat, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Sylvain Poux, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Bernd Roechert, Michel Schneider, Christian Sigrist, Karin Sonesson, Sylvie Staehli, Eleanor Stanley, André Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Anne-Lise Veuthey
EBIRolf Apweiler, Maria Jesus Martin, Claire O'Donovan, Michele Magrane, Yasmin Alam-Faruque, Ricardo Antunes, Benoit Bely, Mark Bingley, David Binns, Lawrence Bower, Wei Mun Chan, Emily Dimmer, Francesco Fazzini, Alexander Fedotov, John Garavelli, Leyla Garcia Castro, Rachael Huntley, Julius Jacobsen, Michael Kleen, Duncan Legge, Wudong Liu, Jie Luo, Sandra Orchard, Samuel Patient, Klemens Pichler, Diego Poggioli, Nikolas Pontikos, Steven Rosanoff, Tony Sawford, Harminder Sehra, Edward Turner, Matt Corbett, Mike Donnelly and Pieter van Rensburg
PIRCathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Winona C. Barker, Chuming Chen, Yongxing Chen, Pratibha Dubey, Hongzhan Huang, Kati Laiho, Raja Mazumder, Peter McGarvey, Darren A. Natale, Thanemozhi G. Natarajan, Jules Nchoutmboube, Natalia V. Roberts, Baris E. Suzek, Uzoamaka Ugochukwu, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh and Jian Zhang
www.uniprot.org
UniProt is mainly supported by the National Institutes of Health (NIH) grant 1 U41 HG006104-01. Additional support for the EBI's involvement in UniProt comes from the NIH grant 2P41 HG02273-07. Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science and the European Commission contracts SLING (226073), Gen2Phen (200754) and MICROME (222886). PIR activities are also supported by the NIH grants 5R01GM080646-04, 3R01GM080646-04S2, 1G08LM010720-01, and 3P20RR016472-09S2, and NSF grant DBI-0850319.
www.isb-sib.ch
Thank you for your attention
http://education.expasy.org/cours/Prague2011/
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