The sequencing of the human genome and intense interest in proteomics and molecular structure have resulted in an explosive need for biological databases. This course surveys a wide range of biological databases and their access tools and enables students to develop proficiency in their use. Databases introduced include genome and sequence databases such as GenBank and Ensemble, as well as protein databases such as PDB and SWISS-PROT. Tools for accessing and manipulating sequence databases such as BLAST, multiple alignment, Perl, and gene finding tools are covered. Specialized databases such as KEGG and HapMap are surveyed for their design and use. The course also focuses on the design of biological databases and examines issues related to heterogeneity, interoperability, complex data structures, object orientation, and tool integration. Students will create their own small database as a course project and will complete homework assignments using biological databases and database tools.
605.205 Molecular Biology for Computer Scientists or equivalent; 605.441 Principles of Database Systems: or 410.634 Practical Computer Concepts for Bioinformatics recommended.