Bioinformatics and Computational Molecular Biology
This course is an introduction to the application of computational methods to biological data analysis and for discovery. The focus will be on computational methods in Genomics and Proteomics.
In Genomics, computational methods will include DNA sequencing and fragment assembly, identification of genes in DNA, gene regulation, expression, large data arrays, and methods to study genetic diversity.
In Proteomics, computational methods will embrace similarity, homology and analogy, protein folding and protein structure.
At the conclusion of the course, the student should understand:
- How DNA sequences can be analyzed to identify genes
- How sequences may be aligned to other similar, but not identical sequences
- How the elements in the sequences may have evolved, and what methods are useful to analyze that evolution
- How 3 dimensional structure and function might be predicted from the sequences
- How the human genome DNA is sequenced
- How technologies can exploit the uniqueness of the genetic sequence in order to build gene detection arrays
- How to apply both classical and modern techniques to detect/discover patterns/motifs in sequence data
There are no rigid prerequisites. It is assumed that the student will have some familiarity with concepts of algorithms and computer basics, elementary biology (particularly DNA, proteins and genes), and rudiments of probability theory. MATLAB is a required tool.
Required Texts
MATLAB: A computer application available at the UConn bookstore for $99. It is also available for use for the semester through the VMware Virtual Computer at Storrs.
Bioinformatics Sequence and Genome Analysis, D.W. Mount, Cold Spring Harbor Laboratory Press 2001 ISBN 0-87969-597-8 (2nd Ed Soft cover).
Suggested Texts
Primer on Molecular Genetics (free download from the Department of Energy).
Introduction to Computational Molecular Biology, J. Setubal and J. Meidanis, PWS Publishing Company, ISBN: 0534952623.
Data Mining Practical Machine Learning Tools and Techniques with JAVA Implementation. IH Witten and E Frank, Morgan Kaufmann Publishers, ISBN.