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Graduate Bioinformatics: Comparative Methods

CBMG 688Q (3 credits) or 688G (2 credit CBMG module)

Spring 2011 ; CBMG688Q (3 credits) & CBMG688G (2 credits)

PLS 1184

Charles F. Delwiche
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This is the public portal for CBMG 688G/Q, Comparative Bioinformatics. There is also a private "Blackboard" site for the class that can be reached by registered students at

Comparative Bioinformatics is intended to serve as a general introduction to bioinformatics and comparative genomics for graduate students in the life sciences including bioengineering; it will also be useful to interested students in the math and computational sciences wishing to learn about biological applications. Students in the course will normally have graduate standing and an advanced background in at least one, and preferably two of the following fields: molecular biology and genetics; evolutionary biology and systematics; and math and computer science. Topics include current and anticipated sequencing technologies, similarity search and pairwise alignment algorithms, contig and genome assembly, gene prediction and finding, functional inference, metagenomics, and annotation.

Comparative Bioinformatics is offered in both a 2-credit and 3-credit version to satisfy the needs of graduate students in different graduate programs. This class qualifies as a BISI/MOCB "module," and can satisfy the BEES requirement in Systematics. Both classes meet together until Spring Break, which marks the end of CBMG 688G. CBMG 688Q meets for the entire semester (but not every class period), and includes a term project.

Graduate students with interests in bioinformatics may also want to consider CBMG688O (Graduate Bioinformatics: Molecular Systematics), which is complementary to Comparative Methods. It would be appropriate to take both CBMG688H and 688O, and students with a strong interest in computational biology are encouraged to do so. If practical, Graduate Bioinformatics: Comparative Methods should be taken prior to Graduate Bioinformatics: Molecular Systematics, but it is acceptable to reverse the order.

Graduate Bioinformatics: Comparative Methods is intended for graduate students interested in the application of computational methods to the comparative analysis of DNA and protein sequences. Students are expected to have a solid background in the biological sciences, but the class is open to students in computer science and related fields who have had some substantial prior exposure to the biological sciences. No prior experience with programming is required, but students should be comfortable working with computers. The primary emphasis will be on understanding the concepts and principles that form the basis for bioinformatic techniques, particularly similarity search and pairwise alignment algorithms (e.g., BLAST, FASTA, Needleman-Wunch, Smith-Waterman), and techniques for homology assessment and functional inference.

Undergraduates should register for BSCI380, "Comparative Bioinformatics" in the Fall Semester.

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