today’s menu: -uniprot - swissprot/trembl -prosite -pfam -gene onltology protein and function...
Post on 21-Dec-2015
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Today’s menu:-UniProt - SwissProt/TrEMBL -PROSITE-Pfam-Gene Onltology
Protein and Function Databases
Tutorial 7
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.
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/
Characterized proteins
Hypothetical proteins
Pfam
• http://pfam.sanger.ac.uk/
•Pfam is a database of multiple alignments of protein domains or conserved protein regions.
One more example
Description
Structure info
Gene Ontology
Links
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
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.
Search Results
Domains architecture
http://www.expasy.ch/tools/pratt/
PRATTMake a pattern from FASTA format sequences inorder to query Prosite
Greed, Overlap and Include
Search A-x(1,3)-A on ABACADAEAFA
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/
Three principal branches
http://www.geneontology.org/amigo/
GO structure is a Directed Acyclic Graph
Important: note what is the source of the GO entry
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