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Analysis of Biological Sequences


East Baltimore
2nd term
3 credits
Academic Year:
2022 - 2023
Instruction Method:
Class Times:
  • Tu Th,  8:30 - 9:50am
Auditors Allowed:
Yes, with instructor consent
Undergrads Allowed:
Grading Restriction:
Letter Grade or Pass/Fail
Course Instructor:
  • Sarah Wheelan
Wheelan, Sarah

With fast-growing technology we can determine the sequences of biological molecules like DNA, RNA, and protein, and can produce tremendous amounts of data. Understanding these sequence data requires hybrid biological, mathematical, and computational expertise. This course presents algorithms and methods for working with and thinking about biological sequences, providing the first steps toward proficiency in this growing field.

Presents a variety of methods for assigning function to biological sequences, emphasizing biologically informed algorithm design. Covers a variety of topics, including low- and high-throughput sequencing history and methods; multiple classes of sequence alignment problems (one-to-one, multiple alignment, alignment of a few sequences to a database, and alignment to a reference genome); interpreting sequence alignments; discovery of patterns in sequences; and visualizing data.

Learning Objectives:

Upon successfully completing this course, students will be able to:

  1. Describe the algorithms used in assigning function to biological sequences;
  2. Determine which methods are appropriate for analyzing sequences derived from different experiments;
  3. Design analysis pipelines that are biologically meaningful and mathematically rigorous.
Methods of Assessment:

Homework 70%, written critique of a publication 30%

Instructor Consent:

No consent required