Tutorial 9 Protein and Function Databases. -UniProt - SwissProt/TrEMBL -PROSITE -Pfam -Gene...
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Transcript of Tutorial 9 Protein and Function Databases. -UniProt - SwissProt/TrEMBL -PROSITE -Pfam -Gene...
Glossary
RepeatA short unit which is unstable in isolation but forms a stable structure when multiple copies are present.
FamilyA collection of related proteins.
UniProt
The Universal Protein Resource (UniProt) is a central repository of protein sequence, function, classification and cross reference.
It was created by joining the information contained in swiss-Prot and TrEMBL.
http://www.uniprot.org/
Pfam
• http://pfam.sanger.ac.uk/
• Pfam is a database of multiple alignments of protein domains or conserved protein regions.
What kind of domains can we find in Pfam?
Trusted Domains
Repeats
Fragment Domains
Nested Domains
Disulfide bonds
Important residues(e.g active sites)
Trans membrane domains
What kind of domains can we find in Pfam?
Low complexity regions
Coiled Coils:(two or three alpha helices that wind around each other)
Context domains: are those that despite not scoring above the family threshold are expected to be real, based on the other domains found in the protein.
Signal peptides:(indicate a protein that will be secreted)
• http://www.expasy.org/tools/scanprosite • ProSite is a database of protein domains and
motifs that can be searched by either regular expression patterns or sequence profiles.
Prosite
Gene Ontology (GO)
• It is a database of biological processes, molecular functions and cellular components.• GO does not contain sequence information nor gene or protein description. • GO is linked to gene and protein databases. •The GO database is structured as a tree
http://www.geneontology.org/
GO sourcesISS Inferred from Sequence/Structural SimilarityIDA Inferred from Direct AssayIPI Inferred from Physical InteractionTAS Traceable Author StatementNAS Non-traceable Author StatementIMP Inferred from Mutant PhenotypeIGI Inferred from Genetic InteractionIEP Inferred from Expression PatternIC Inferred by CuratorND No Data availableIEA Inferred from electronic annotation
DAVID Functional Annotation Bioinformatics Microarray Analysis
• Identify enriched biological themes, particularly GO terms• Discover enriched functional-related gene/protein groups• Cluster redundant annotation terms• Explore gene names in batch