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Tutorial 9

Tutorial 9. Protein and Function Databases. Protein and Function Databases. UniProt - SwissProt/TrEMBL PROSITE Pfam Gene Onltology DAVID. Glossary. Domain A structural unit which can be found in multiple protein contexts. Glossary. Repeat

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Tutorial 9

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  1. Tutorial 9 Protein and Function Databases

  2. Protein and Function Databases UniProt - SwissProt/TrEMBL PROSITE Pfam Gene Onltology DAVID

  3. Glossary Domain A structural unit which can be found in multiple protein contexts.

  4. Glossary 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.

  5. 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.

  6. Protein search Uniprot input Reviewed protein

  7. Sequence download Uniprot output Accession number Protein status organism length

  8. Information for one protein General information annotations

  9. General keywords GO annotation (MF, BP, CC)

  10. Alternative splicing isoforms Features in the sequence

  11. Sequences References

  12. Alignment for two or more proteins

  13. MSA

  14. Blast

  15. Pfam • http://pfam.sanger.ac.uk/ • Pfam is a database of multiple alignments of protein domains or conserved protein regions.

  16. 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

  17. 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)

  18. Pfam input

  19. Domains Domain range and score

  20. Description Structure info Gene Ontology Links

  21. Prosite • http://www.expasy.org/tools/scanprosite • ProSite is a database of protein domains and motifsthat can be searched by either regular expression patterns or sequence profiles.

  22. Search Results Domains architecture

  23. Gene Ontology (GO) http://www.geneontology.org/ • 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

  24. Search by AmiGO

  25. Three principal branches http://www.geneontology.org/amigo/

  26. GO structure is a Directed Acyclic Graph

  27. GO sources ISS Inferred from Sequence/Structural Similarity IDA Inferred from Direct Assay IPI Inferred from Physical Interaction TAS Traceable Author Statement NAS Non-traceable Author Statement IMP Inferred from Mutant Phenotype IGI Inferred from Genetic Interaction IEP Inferred from Expression Pattern IC Inferred by Curator ND No Data available IEA Inferred from electronic annotation

  28. Results for alpha-synuclein

  29. 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 

  30. annotation classification ID conversion

  31. Functional annotation Upload Annotation options

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