Today’s menu: -UniProt - SwissProt/TrEMBL -PROSITE -Pfam -Gene Onltology Protein and Function...
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Transcript of Today’s menu: -UniProt - SwissProt/TrEMBL -PROSITE -Pfam -Gene Onltology Protein and Function...
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Today’s menu:-UniProt - SwissProt/TrEMBL -PROSITE-Pfam-Gene Onltology
Protein and Function Databases
Tutorial 7
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Glossary
Domain- A structural unit which can be found in multiple protein contexts.Motif- A short unit found outside globular domains.Repeat- A short unit which is unstable in isolation but forms a stable structure when multiple copies are present.Family- A collection of related proteins.
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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/
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Characterized proteins
Hypothetical proteins
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Pfam
• http://pfam.sanger.ac.uk/
•Pfam is a database of multiple alignments of protein domains or conserved protein regions.
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One more example
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Description
Structure info
Gene Ontology
Links
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What kind of domains can we find in Pfam?
Trusted Domains
Repeats and Motifs
Fragment Domains
Nested Domains
Disulfide bonds
Important residues(e.g active sites)
Trans membrane domains
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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)
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• 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.
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Search Results
Domains architecture
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http://www.expasy.ch/tools/pratt/
PRATTMake a pattern from FASTA format sequences inorder to query Prosite
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Greed, Overlap and Include
Search A-x(1,3)-A on ABACADAEAFA
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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/
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Three principal branches
http://www.geneontology.org/amigo/
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GO structure is a Directed Acyclic Graph
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Important: note what is the source of the GO entry
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GO sources
ISS 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