EBI is an Outstation of the European Molecular Biology Laboratory. UniProt Jennifer McDowall, Ph.D....

EBI is an Outstation of the European Molecular Biology Laboratory.

UniProt

Jennifer McDowall, Ph.D.Senior InterPro Curator

Protein Sequence Database:

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


Sequence quality in UniProt

Evidence at protein level

Evidence at transcript level

Inferred from homology

Predicted

Uncertain

Protein existence level Human

59%

37.5%

1%

0.5%

2%


UniProt Consortium


3 Components of UniProt

UniProtKBUniProtKBKnowledgebase

UniRefUniRefReference

Cluster

UniParcUniParcProtein 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


EMBL/GenBank/DDBJ, Ensembl, PDB, RefSeq, Patent data, Model organism databases


UniProtKB pipeline

EMBL

CGCGCCTGTACGCTGAACGCTCGTGACGTGTAGTGCGCGCGCTGTGATAGCG

CTGATCGTGATGCGTATGCAGGTCGT

nucleotide sequencingnucleotide sequencing

TrEMBL

translate translate sequencesequence

UniProtKBUniProtKB

Swiss-Protannotationannotation

EBI EBI SIB SIB PIRPIR

>7M >4K


Searching UniProt:

Simple text search


Searching UniProt

http://www.uniprot.org/

Search tools include:

• Text Search

• Blast sequence search

• Additional search engines through EBI (e.g. MPSearch and FASTA)


Searching UniProt – Simple Search

• Text-based searching• Logical operators ‘&’ (and), ‘|’


Searching UniProt – Simple Search


Searching UniProt – Search Results

Each linked to the UniProt entry


Searching UniProt – Search Results


EXERCISE 1


Exploring a SwissProt entry:

General information


Sequence Sequence features

Ontologies

ReferencesNomenclature

Splice variants

Annotations


UniProt/Swiss-Prot AnnotationRemove 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 databasesBibliography 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


Customise layoutCollapse section


UniProtKB/Swiss-Prot Annotation


Hold down cursor to drag-and-drop sections

Customise layout


Customise layout


Entry Information

Swiss-Prot removes redundancy


Entry InformationSequence correction, versioning and archiving



Merged A8K2S6 with Q00987

Able to compare versions directly



For example: erroneous gene model predictions, frameshifts,read-throughs, premature stop codons, erroneous initiator Met…


Names and OriginSome literature search engines pull synonyms from UniProt


EXERCISE 2



Sequence annotation


Sequence


Sequence variation - conflicts


Sequence variation – splicing


Annotate Sequence


EXERCISE 3



Structural annotation


Structure - secondary


Structure - tertiary



Provides information on ordered and disordered regions of protein


Structure - quaternary


EXERCISE 4



General annotation


General Annotation

Controlled vocabularies used where possible

References provides

Literature-derived annotation


General AnnotationAdditional annotation from Gene Ontology


Modifications


Disease Association


Disease Association

Mendelian Inheritance in Man provides information on genetic

disease associations

Pharmacogenomics database


Disease Association


Similarity


Binary Interactions

Interacting protein

Experimental information in IntAct

Data imported from other sources


Binary Interactions

Database of Interacting Proteins

Pathway databases

Data imported from other sources


Cross ReferencesA central portal to a wealth of external resources…


Source references included


Classification and domain annotation provided by InterPro


A wealth of external links


EXERCISE 5


Searching UniProt:

BLAST search


Searching UniProt – Blast Search


Searching UniProt – Blast Results

Alignment with query sequence



Aligns checked sequences


EXERCISE 6


Exploring a UniProt/TrEMBL

entry


UniProt/TrEMBL entry

Redundancy

Nucleotide dataAutomatic 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:


Transferred annotation


EXERCISE 7

http://www.ebi.ac.uk

Acknowledgements

Rolf Apweiler

Amos Bairoch

Cathy Wu

+100 annotators

EBI is an Outstation of the European Molecular Biology Laboratory. UniProt Jennifer McDowall, Ph.D....

Documents

Transcript of EBI is an Outstation of the European Molecular Biology Laboratory. UniProt Jennifer McDowall, Ph.D....