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EBI is an Outstation of the European Molecular Biology Laboratory. UniProt Jennifer McDowall, Ph.D. Senior InterPro Curator Protein Sequence Database:

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Presentation on theme: "EBI is an Outstation of the European Molecular Biology Laboratory. UniProt Jennifer McDowall, Ph.D. Senior InterPro Curator Protein Sequence Database:"— Presentation transcript:

1 EBI is an Outstation of the European Molecular Biology Laboratory. UniProt Jennifer McDowall, Ph.D. Senior InterPro Curator Protein Sequence Database:

2 http://www.ebi.uniprot.org What do protein scientists require? High quality protein sequence Non-redundant data with maximal coverage, including splice isoforms, disease variants and PTMs. Protein identification Protein annotation Stable identifiers and consistent nomenclature Detailed information: protein function, biological processes, molecular interactions, and pathways Sequence archiving essential

3 http://www.ebi.uniprot.org Sequence quality in UniProt Evidence at protein level Evidence at transcript level Inferred from homology Predicted Uncertain Protein existence levelHuman 59% 37.5% 1% 0.5% 2%

4 http://www.ebi.uniprot.org UniProt Consortium

5 http://www.ebi.uniprot.org 3 Components of UniProt UniProtKB Knowledgebase UniRef Reference Cluster UniParc Protein Archive  Protein sequence repository  Swiss-Prot: non-redundant, manually annotated  TrEMBL: redundant, automatically annotated  History of all sequences  Combines sequences (speed searching)  UniRef100, UniRef90, UniRef50

6 http://www.ebi.uniprot.org EMBL/GenBank/DDBJ, Ensembl, PDB, RefSeq, Patent data, Model organism databases

7 http://www.ebi.uniprot.org UniProtKB pipeline EMBL CGCGCCTGTACGC TGAACGCTCGTGA CGTGTAGTGCGCG CGCTGTGATAGCG CTGATCGTGATGC GTATGCAGGTCGT nucleotide sequencing TrEMBL translate sequence UniProtKB Swiss-Protannotation EBI SIB PIR >7M >4K

8 http://www.ebi.uniprot.org Searching UniProt: Simple text search

9 http://www.ebi.uniprot.org Searching UniProt http://www.uniprot.org/ Search tools include: Text Search Blast sequence search Additional search engines through EBI (e.g. MPSearch and FASTA)

10 http://www.ebi.uniprot.org Searching UniProt – Simple Search Text-based searching Logical operators ‘&’ (and), ‘|’

11 http://www.ebi.uniprot.org Searching UniProt – Simple Search

12 http://www.ebi.uniprot.org Searching UniProt – Search Results Each linked to the UniProt entry

13 http://www.ebi.uniprot.org Searching UniProt – Search Results

14 http://www.ebi.uniprot.org Searching UniProt – Search Results

15 http://www.ebi.uniprot.org EXERCISE 1

16 http://www.ebi.uniprot.org Exploring a SwissProt entry: General information

17 http://www.ebi.uniprot.org SequenceSequence features Ontologies References Nomenclature Splice variants Annotations

18 http://www.ebi.uniprot.org UniProt/Swiss-Prot Annotation Remove redundancy  Merge TrEMBL (1 gene product 1 entry) Sequence variation  Identify conflicts & alternative splicing Modifications  Posttranslational, e.g. carbohydrates Annotate sequence  Map domains and sites onto sequence General annotation  Descriptive comments, e.g. function Binary interactions  Linked to protein-protein interaction data Cross references  Extensive integration with other databases Bibliography  Cited references Taxonomy  Description of biological source Structure  Describes both secondary and quaternary Disease association  Map sequence deficiencies causing disease Similarity  To protein families and domains

19 http://www.ebi.uniprot.org Customise layout Collapse section

20 http://www.ebi.uniprot.org UniProtKB/Swiss-Prot Annotation

21 http://www.ebi.uniprot.org Hold down cursor to drag-and-drop sections Customise layout

22 http://www.ebi.uniprot.org Customise layout

23 http://www.ebi.uniprot.org Entry Information Swiss-Prot removes redundancy

24 http://www.ebi.uniprot.org Entry Information Sequence correction, versioning and archiving

25 http://www.ebi.uniprot.org Entry Information Sequence correction, versioning and archiving Merged A8K2S6 with Q00987 Able to compare versions directly

26 http://www.ebi.uniprot.org Entry Information Sequence correction, versioning and archiving

27 http://www.ebi.uniprot.org Entry Information Sequence correction, versioning and archiving For example: erroneous gene model predictions, frameshifts, read-throughs, premature stop codons, erroneous initiator Met…

28 http://www.ebi.uniprot.org Names and Origin Some literature search engines pull synonyms from UniProt

29 http://www.ebi.uniprot.org EXERCISE 2

30 http://www.ebi.uniprot.org Exploring a SwissProt entry: Sequence annotation

31 http://www.ebi.uniprot.org Sequence

32 http://www.ebi.uniprot.org Sequence

33 http://www.ebi.uniprot.org Sequence variation - conflicts

34 http://www.ebi.uniprot.org Sequence variation – splicing

35 http://www.ebi.uniprot.org Sequence variation – splicing

36 http://www.ebi.uniprot.org Sequence variation – splicing

37 http://www.ebi.uniprot.org Annotate Sequence

38 http://www.ebi.uniprot.org EXERCISE 3

39 http://www.ebi.uniprot.org Exploring a SwissProt entry: Structural annotation

40 http://www.ebi.uniprot.org Structure - secondary

41 http://www.ebi.uniprot.org Structure - secondary

42 http://www.ebi.uniprot.org Structure - tertiary

43 http://www.ebi.uniprot.org Structure - tertiary

44 http://www.ebi.uniprot.org Structure - tertiary Provides information on ordered and disordered regions of protein

45 http://www.ebi.uniprot.org Structure - tertiary

46 http://www.ebi.uniprot.org Structure - quaternary

47 http://www.ebi.uniprot.org EXERCISE 4

48 http://www.ebi.uniprot.org Exploring a SwissProt entry: General annotation

49 http://www.ebi.uniprot.org General Annotation Controlled vocabularies used where possible References provides Literature-derived annotation

50 http://www.ebi.uniprot.org General Annotation Additional annotation from Gene Ontology

51 http://www.ebi.uniprot.org Modifications

52 http://www.ebi.uniprot.org Disease Association

53 http://www.ebi.uniprot.org Disease Association Mendelian Inheritance in Man provides information on genetic disease associations Pharmacogenomics database

54 http://www.ebi.uniprot.org Disease Association

55 http://www.ebi.uniprot.org Similarity

56 http://www.ebi.uniprot.org Similarity

57 http://www.ebi.uniprot.org Binary Interactions Interacting protein Experimental information in IntAct Data imported from other sources

58 http://www.ebi.uniprot.org Binary Interactions Database of Interacting Proteins Pathway databases Data imported from other sources

59 http://www.ebi.uniprot.org Cross References A central portal to a wealth of external resources…

60 http://www.ebi.uniprot.org Cross References A central portal to a wealth of external resources…

61 http://www.ebi.uniprot.org Source references included

62 http://www.ebi.uniprot.org Classification and domain annotation provided by InterPro

63 http://www.ebi.uniprot.org A wealth of external links

64 http://www.ebi.uniprot.org EXERCISE 5

65 http://www.ebi.uniprot.org Searching UniProt: BLAST search

66 http://www.ebi.uniprot.org Searching UniProt – Blast Search

67 http://www.ebi.uniprot.org Searching UniProt – Blast Search

68 http://www.ebi.uniprot.org Searching UniProt – Blast Results Alignment with query sequence

69 http://www.ebi.uniprot.org Searching UniProt – Blast Results

70 http://www.ebi.uniprot.org Searching UniProt – Blast Results Aligns checked sequences

71 http://www.ebi.uniprot.org Searching UniProt – Blast Results

72 http://www.ebi.uniprot.org EXERCISE 6

73 http://www.ebi.uniprot.org Exploring a UniProt/TrEMBL entry

74 http://www.ebi.uniprot.org UniProt/TrEMBL entry Redundancy  Nucleotide data Automatic clean-up  InterPro family classification  Cross-references  Keywords (common annotation with Swiss-Prot)  Transfers common annotation to related family members in TrEMBL Automatic annotation Swiss-Prot = 400K TrEMBL = 6M Entries:

75 http://www.ebi.uniprot.org Transferred annotation

76 http://www.ebi.uniprot.org EXERCISE 7

77 http://www.ebi.ac.uk Acknowledgements Rolf Apweiler Amos Bairoch Cathy Wu +100 annotators


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