Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Gene therapy of the human retina wikipedia , lookup
Neuronal ceroid lipofuscinosis wikipedia , lookup
Gene expression programming wikipedia , lookup
Gene expression profiling wikipedia , lookup
Epigenetics of neurodegenerative diseases wikipedia , lookup
Gene nomenclature wikipedia , lookup
Point mutation wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Tutorial 7 Protein and Function Databases Today’s menu: -UniProt - SwissProt/TrEMBL -PROSITE -Pfam -Gene Onltology Hypothetical proteins Characterized proteins UniProt http://www.uniprot.org/ 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 • http://pfam.sanger.ac.uk/ • 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? 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) Low complexity regions Coiled Coils: (two or three alpha helices that wind around each other) • 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 PRATT Make a pattern from FASTA format sequences http://www.expasy.ch/tools/pratt/ 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 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 IDA IPI TAS NAS IMP IGI IEP IC ND IEA Inferred from Sequence/Structural Similarity Inferred from Direct Assay Inferred from Physical Interaction Traceable Author Statement Non-traceable Author Statement Inferred from Mutant Phenotype Inferred from Genetic Interaction Inferred from Expression Pattern Inferred by Curator No Data available Inferred from electronic annotation