Molecular Biophysics & Biochemistry 447b3 / 747b3 Bioinformatics
Relational Databases
Unstructured Data
Semi-Structured Data
Structured Data
SQL
matches table
matches table 2
structures table
folds table
Table Interpretation
Structure of a Table
What is a Key?
SQL Select on a Single Table
SQL Select on a Single Table, Example
SQL Select on a Single Table, Example 2
Joins
SQL Select on Multiple Tables
Foreign Key
Selection as Array Lookup
SQL Select on Multiple Tables
Cross Product A x B
ER-diagrams
Aggregate Functions-- Statistics on Attributes
Joins
Join Gives Unnormalized Table
Normalization
Normalization Example
Normalized Tables
Query Optimization
Indexes Speed Access
Object Databases
Forms & reports [user views]
Example Report: Motions Database
Example Report: Motions Database
Example Report: Motions Database
Example Report: Motions Database
Example Report: Motions Database
Example Report: Motions Database
Packing Based Classification
Packing Based Classification: Hinge v Shear
Simple Forms Example: Links Page
Aspects of Forms: Transactions and Security
Large-scale Example: Census DB
Molecular Biology Information: Whole Genomes
Explonential Growth of Data Matched by Development of Computer Technology
Major Application II: Overall Genome Characterization
Shared Folds in Genomes are a/b
What are the Most Common Folds in the Genomes? How many of these are shared?
5 Folds in Top-10 All 3 Genomes
TM-helix “prediction”
2º Structure Prediction
Supersecondary structure words
Complex Data Example: Encoding Trees in RDBs
RDBs Everywhere: Internet Mail
RDBs Everywhere: File System