[email protected] swiss-prot group, geneva sib swiss institute of bioinformatics
DESCRIPTION
The UniProt knowledgebase www.uniprot.org a hub of integrated protein data http://education.expasy.org/cours/Turin/. [email protected] Swiss-Prot group, Geneva SIB Swiss Institute of Bioinformatics. Protein sequences. - PowerPoint PPT PresentationTRANSCRIPT
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[email protected] group, GenevaSIB Swiss Institute of Bioinformatics
The UniProt knowledgebase
www.uniprot.org
a hub of integrated protein data
http://education.expasy.org/cours/Turin/
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Protein sequences
• > 180 billions of ‘different’ proteins on earth (∑ N species x M genes)
• > 23.0 millions of ‘known and public’ protein sequences in 2012
• More than 99 % of the protein sequences are derived from the translation of nucleotide sequences (mRNA or DNA)
• About 1 % come from direct protein sequencing (Edman, MS/MS…)
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Science cover, february 2011
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protein sequence functional information
data knowledge
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UniProt consortium
EBI : European Bioinformatics Institute (UK)SIB : Swiss Institute of Bioinformatics (CH)PIR : Protein information resource (US)
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www.uniprot.org
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UniProt databases
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UniProt databases
UniParcUniParc: protein sequence archive (EMBL-ENA equivalent at the protein level) Each entry contains a protein sequence, taxonomic information, cross-links to other databases where you find the sequence (active or not)
No annotation
All the public patented sequences are stored in UniParc (EPO, USPO, JPO)
You can: query, Blast, download
~31 mo entries
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UniProt databases
UniRefUniRef
3 clusters of protein sequences with 100, 90 and 50 % identity;
useful to speed up sequence similarity search (BLAST)
You can: query, Blast, download
UniRef100 17 mo entries; UniRef90 11 mo entries; UniRef50 5 mo entries
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UniProt databases
UniMESUniMES:
protein sequences derived from metagenomic projects (mostly Global Ocean Sampling (GOS))
You can : download
12 mo entries, included in UniParc
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UniProt databasesThe centerpiece
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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
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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 (includes direct protein sequencing)
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 %
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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
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UniProtKB/TrEMBL
unreviewedAutomatic annotation
released every 4 weeks
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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
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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))
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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
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UniProtKB/Swiss-Prot
reviewedmanually annotated
released every 4 weeks
Manual biocuration is essential to knowledge maintenance
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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
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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, …)
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UniProtKB/Swiss-Prot
1- Protein sequence curation
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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
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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’
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UCSC genome browserexamples of CDS annotation submitted to INSDC…
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UniProtKB/Swiss-Prot
2- Biological data curation
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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
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Protein and gene names
Synonyms useful for
literature searching
Synonyms useful for
literature searching
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…enable researchers to obtain a summary of what is known about a protein…
General annotation
(Comments)
www.uniprot.org
An evidence attribution system allows to easily trace the source of each annotation(Reference number, By similarity, Probable, Potential)
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Human protein manual annotation: some statistics (June 2012)
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Sequence annotation
(Features)
…enable researchers to obtain a summary of what is known about a protein…
www.uniprot.org
An evidence attribution system allows to easily trace the source of each annotation(Reference number, By similarity, Probable, Potential)
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Find all the proteins localized in the cytoplasm (experimentally
proven) which are phosphorylated on a serine (experimentally proven)
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Ontologies
www.uniprot.org
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• 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
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Not sequence validation !
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UniProtKB
Additional information can be found in the cross-references
(to more than 140 databases)
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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
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The UniProt web site The UniProt web site www.uniprot.orgwww.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
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Search
A very powerful text search tool with autocompletion and refinement
options allowing to look for UniProt entries and documentation by
biological information
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The search interface guides users with helpful suggestions and hints
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Result pages: highly customizableResult pages: highly customizable
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Result pages: downloadableResult pages: downloadable
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The URL can be bookmarked and
manually modified.
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Query: sequence:(database:epo OR database:JPO or database:USPTO)
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Blast
A tool associated with the standard options to search
sequences in different UniProt databases and
data sets
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Blast: customize the result display
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Blast: local alignment
sequence annotation highlighting option
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Align
A ClustalW multiple alignment tool with
sequence annotation highlighting option
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Align
sequence annotation highlighting option
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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.
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Query your own dataset
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ID Mapping
Gives the possibility to get a mapping between different databases for a given
protein
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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.
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Download
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Download UniProt Download UniProt http://www.uniprot.org/downloadshttp://www.uniprot.org/downloads
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The UniProt ConsortiumThe 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
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UniProt is mainly supported by the National National Institutes of Health (NIH)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 Swiss Federal Government through the Federal Office of Education and Science and the European CommissionEuropean 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 NSFNSF grant DBI-0850319.
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www.isb-sib.chwww.isb-sib.ch
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Thank you for your attentionThank you for your attention
http://education.expasy.org/cours/Turin/
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Some pratical issueswww.uniprot.org
• Look for HBB – customize display - multiple alignment
• Look for plant protein sequence similar to human HBB (Blast).
• ID mapping: Several proteins have been identified in a proteomic
experiment. Which GO terms do they share? (GI numbers of the identified proteins: 16130093, 20664033, 1789812, 27574045, 229597766).
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Summary
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A few words on the UniProt ‘complete proteome’
sequence sets…
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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 UniProtKB - complete proteomesproteomes
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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 UniProtKB - complete proteomesproteomes
Additional information: www.uniprot.org/faq/15
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Query UniProtKB + download
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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…