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The MoBIoS Project Mo lecular B iological I nformation S ystem

M o B I o S M o B I o S. S o I B o M S o I B o M. The MoBIoS Project Mo lecular B iological I nformation S ystem. Daniel P. Miranker University of Texas. Rui Mao, Weijia Xu, Wenguo Liu, Willard Briggs, Smriti Ramakrishnan, Shu Wang, Francois Barbancon, Shulin Ni.

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The MoBIoS Project Mo lecular B iological I nformation S ystem

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  1. M o B I o S M o B I o S S o I B o M S o I B o M The MoBIoS ProjectMolecular Biological Information System Daniel P. Miranker University of Texas Rui Mao, Weijia Xu, Wenguo Liu, Willard Briggs, Smriti Ramakrishnan, Shu Wang, Francois Barbancon, Shulin Ni

  2. Bioinformatics Problem: Must scan entire database, O(n), to find data matching the most basic of patterns. Compare two genome  O(n2) Solution: MoBIoS: A Metric-Space DBMS • Metric space index enables O(log n) retrieval time • Sequences • Mass-spectra • Protein Structure • Combi-chem Libraries

  3. Metric Space is • a pair, M=(D,d), where • D is a set of points • d is [metric] distance function with the following properties: • d(x, y) = d (y, x) (symmetry) • d(x, y) > 0, d(x, x) = 0 (non negativity) • d(x, y)  d(x, z) + d(z, y) (triangle inequality)

  4. Metric-Space Indexing Materialize Hierarchical Clustering as a Tree-Based Data Structure C A B A E B C D E F D F

  5. Active Application Efforts Other Opportunities Mass-Spec Protein Identification De novo Protein Sequencing Combi-Chem Library Management Compartive and Phylo Genomics Homology Search MoBIoS SQL (M-SQL) Query Engine Mining Engine MoBIoS Java Interface (MJI) Metric-Space Based Storage Manager DNA Sequences Peptide Sequences Mass-Spec. Signatures Small Molecule & Protein Libraries MoBIoS Architecture(Molecular Biological Information System) • mSQL, simple SQL extensions enabling fast, consice bioinformatic programming. • Integrated repository for diverse biologicial data types.

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