3 Information Retrieval

3 Information Retrieval - 1 Introduction to Bioinformatics...

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1 Introduction to Bioinformatics/ Elements of Bioinformatics Information Retrieval
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2 Protein family databases • Conserved sequences in groups of related protein sequences are converted into diagnostic patterns • Searching protein pattern databases is more sensitive and selective than searching sequence database in assigning functions to a new protein sequence.
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3 Attwood, T.K. (2000) The quest to deduce protein function from sequence: the role of pattern databases. The International Journal of Biochemistry and Cell Biology 32: 139-155. Three main methods for building pattern databases: 1. Single motif methods 2. Multiple motifs methods 3. Full domain alignment methods
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4 Protein Stored information Family Database PROSITE Regular expressions (patterns) PRINTS Frequency matrices (fingerprints) BLOCKS Position-specific weight matrices (blocks) Profiles Gapped weighted matrices (profile) Pfam Hidden Markov Models (HMMs)
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5 InterPro • Integration of PROSITE, PRINTS, Pfam, ProDom, SMART and TIGRFAMs, PIRSF, SuperFamily, PANTHER, Gene3D databases. (http://www.ebi.ac.uk/interpro/)
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6 http://www.geneontology.org/
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7 Gene Ontology Controlled vocabularies (ontologies) for annotation of gene products in any organism 3 sets of vocabulary: cellular component • describe locations, at the levels of sub-cellular structures and macromolecular complexes • e.g. mitochondrial matrix biological process • a recognized series of events or molecular functions • e.g. oxidative phosphorylation molecular function • describes activities, such as catalytic or binding activities, that occur at the molecular level. • e.g. oxidoreductase activity
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8 GO structure • GO terms can be linked by five types of relationships: is_a (a simple class-subclass relationship) • A is_a B means A is a subclass of B • e.g. cation binding is_a ion_binding part_of • C part_of D means that whenever C is present, it is always a part of D, but C does not always have to be present. • e.g. nuclear envelop part_of endomembrane system regulates ; positively_regulates ; negatively_regulates • When a biological process E regulates a function or a process F, it modulates the occurrence of F
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9 An example of relationships between GO terms
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10 • Human glucocorticoid receptor (GCR_human) annotated with GO terms: molecular function transcription factor activity GO:0003700 molecular function protein binding GO:0005515
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This note was uploaded on 07/29/2010 for the course BIOC BIOC1805 taught by Professor Dr.brianwong during the Summer '09 term at HKU.

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3 Information Retrieval - 1 Introduction to Bioinformatics...

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