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Comparative Bioinformatics

BSCI 348S

Catalog Description

Computational methods for study of biological sequence data in comparative biology and evolution. Analysis of genome content and organization. Techniques for searching sequence databases, pairwise and multiple sequence alignment, phylogenetic methods, and methods for pattern recognition and functional inference from sequence data.

Course Description

Genomes are tremendously complex, naturally evolved information storage devices. Techniques in DNA sequencing have made it practical to fully sequence entire genomes, and this has led to the more difficult problem of understanding the information that is contained within these genomes. This has led to a new field that incorporates elements of molecular biology, evolutionary biology, and computer science. Molecular biology provides the molecular tools to determine DNA sequences and asks fundamental questions about how the genetic components interact, evolutionary biology provides the conceptual framework to understand the change in sequences over time, and computer science provides the information processing needed to extract useful information from genome sequences.

This course will provide an introduction to the kinds of information that are available from DNA sequencing projects, ranging from the sequences of individual genes to those of entire genomes. There will be two core themes in the class: the analytical techniques that can be used to evaluate sequence data, and examples of the biological significance of such analyses. These themes will be intertwined within the class, typically with clusters of 2-4 lectures that emphasize analytical and algorithmic issues, followed by a similar number of more topical lectures addressing the biological issues addressed by sequence analysis. The central goal of the course will be to train students to think effectively about DNA sequences as a problem in information processing.

The course will be in a MWF lecture format, with the Friday sessions held as computer practica. Assessment will be with two midterm exams, a series of 4-5 homework assignments equal in cumulative weight to a midterm, and a final exam.

The course will have strong elements of molecular biology, evolutionary biology, and computer science. There is no comparable class at the University of Maryland – College Park. It is anticipated that this course will become a core course in the developing Bioinformatics program. The most closely related course would be Molecular Evolution, but this course will more strongly emphasize DNA sequence data and their analysis, and will take a more macroevolutionary approach; there will be relatively little overlap between the courses, and a student would certainly benefit from taking both of them.

Prerequisites: BSCI 222 and Math 221, or consent of instructor.

Recommended courses: BSCI 370 (Introduction to Evolution)

Text: Mount, David W., 2001. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

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