1. The MoBIoS Project Molecular 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(n 2 ) Solution: MoBIoS: A Metric-Space DBMS –Metric space index enables O(log n) retrieval time – Protein Structure – Combi-chem Libraries –Sequences –Mass-spectra

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 D E F A B B F D E A C

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