Spring 1998 Course Offering
Bioinformatics and Genome Analysis
BCHE 451/MOLB 550/EPWS 451 3 Cr.
TIME: 2:30 to 5 Wednesdays
PLACE: Chem 201
INSTRUCTORS: Peter Lammers & Craig Liddell
Every field of biology has been revolutionized by the availability of DNA sequence information. The sheer volume of this data is currently exceeding our capacity to critically evaluate it. Embedded in the seemingly simple linear sequence of the four nucleotides in DNA are more complex levels of information: encrypted codes for all subcellular, cellular, organ, organismal and even ecological and population-level functions. The goal of computational biology is nothing less than the complete understanding of these codes. The objective of this course is to provide an introductory overview of the computation problems and methods being applied to the problem.
The course will focus on three related issues:
1. sequencing strategies and methods (e.g. whole genomes, expressed sequence tags, and deep cDNA projects).
2. computational discovery methods for genome annotation.
3. validation studies comparing predictions to experiment.
Emphasis will be placed on the biological rationale underpinning many widely used algorithms. Computational design and implementation issues will be covered for a select few. Fields to be covered include primary sequence comparision methods (FASTA, BLAST and BLOCKS), secondary structure prediction algorithms and and overview of emerging field of homology modeling. The problem of gene discovery in genomic sequence requires a solution to the dificult problem of recognition of exon/intron boundaries. The best available algorithms in this area will be presented including GeneScan, GenMark and several others.
An overview of important computational issues related to bioinformatics will also be presented. Topics will include file transfer and manipulation, string handling using PERL for I/O, and principals of database design and development.
We hope to offer students practical experience with proprietary software being used for sequence project assembly, management and analysis (Sequencher 3.0). Additional group and individual projects will involve using WEB based versions of the programs listed above. Finally students will be encouraged and expected to brouse the Internet resources to indentify and critically evaluate additional sites and capabilities.
Prerequisites: undergraduates: two semesters of undergraduate biochemistry (eg. BCHE 395, 396) at least one CS course (eg. CS110 or a programming course). Graduates: undergraduate biochemistry and molecular genetics or concurrent enrollment in CHEM/MOLB 545 Molecular and Biochemical Genetics, and a computer science course as for undergraduates.