Today’s menu: -UniProt - SwissProt/TrEMBL -PROSITE -Pfam -Gene Onltology Protein and Function Databases Tutorial 7.

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Presentation transcript:

Today’s menu: -UniProt - SwissProt/TrEMBL -PROSITE -Pfam -Gene Onltology Protein and Function Databases Tutorial 7

Characterized proteins Hypothetical 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.

Pfam Pfam is a database of multiple alignments of protein domains or conserved protein regions.

One more example

ls mode: a hit is reported if it globally aligns to the seed fs mode: a hit is reported if it locally aligns to the seed

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)

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

PRATT Make a pattern from FASTA format sequences

PRATT

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

Three principal branches

GO structure is a Directed Acyclic Graph

Important: note what is the source of the GO entry

GO sources ISSInferred from Sequence/Structural Similarity IDAInferred from Direct Assay IPIInferred from Physical Interaction TASTraceable Author Statement NASNon-traceable Author Statement IMPInferred from Mutant Phenotype IGIInferred from Genetic Interaction IEPInferred from Expression Pattern ICInferred by Curator NDNo Data available IEAInferred from electronic annotation