COMP 571 BIOINFORMATICS: SEQUENCE ANALYSIS
Spring 2015
(For Fall 2010 offering, which was focused mostly on population genetics, click here.)

Staff

Course Information

• MEETING PLACE AND TIME: Herzstein Hall 210, Tuesday and Thursday, 2:30-3:45.
• TEXTBOOKS (none required, but highly recommended):
  • "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids", by Durbin et al., Cambridge University Press.
  • "Algorithms on Strings, Trees, and Sequences", by Gusfield. Cambridge University Press.
  • "Understanding Bioinformatics", by M. Zvelebil and J.O. Baum. Published by Garland Science, 2008.
  • "Population Genetics", by M.B. Hamilton. Published by Wiley-Blackwell, 2009.
  • An Introduction to Population Genetics Theory, by Crow and Kimura.
  • Inferring Phylogenies, by Felsenstein.
  • Fundamentals of Molecular Evolution, by Graur and Li.
  • Theoretical Evolutionary Genetics, by Felsenstein (PDF available online).
  • Evolutionary Theorey: Mathematical and Conceptual Foundations, by Rice.
• SOFTWARE: here are links to programs (Matlab toolboxes included) that may be useful for homework tasks, and beyond:
  1. For a comprehensive list of phylogeny programs, please see the website maintained by Prof. Joe Felsenstein here.
  2. The Molecular Biology and Evolution toolbox. Click here for a paper that describes the tool.
  3. The Population Genetics and Evolution toolbox.
  4. The ms tool for generating samples under neutral models.
• INTENDED AUDIENCE: anyone who's interested in learing about exciting developments at the intersection of evolutionary biology and computing. It is expected the students have had an algorithms course, can program, and are not afraid of math (if you do not satisfy at least one of these three, this course is not for you!). Knowledge of biology is a plus, but is not required. This is not a "programming for biologists" course, nor is it a course on how to use bioinformatics tools and databases.
• TOPICS TO BE COVERED (tentative, time permitting):
  1. Pairwise sequence alignment
  2. Markov chains and HMMs
  3. Pairwise alignment using HMMS
  4. Profile HMMs for sequence families
  5. Multiple sequence alignment
  6. Phylogenetic tree inference
  7. Phylogenomics
  8. Suffix trees
  9. The Burrows-Wheeler transform
  10. Genome characteristics and annotation
  11. Stochastic context-free grammars and RNA secondary structure prediction
• GRADING:
  • The grades will be based on:
    • A set of homework assignments (30%).
    • A project (30%).
    • Midterm 1 (20%): in-class on 26 February 2015.
    • Midterm 2 (20%): in-class on 23 April 2015.
• RICE HONOR CODE: In this course, all students will be held to the standards of the Rice Honor Code, a code that you pledged to honor when you matriculated at this institution. If you are unfamiliar with the details of this code and how it is administered, you should consult the Honor System Handbook. This handbook outlines the University's expectations for the integrity of your academic work, the procedures for resolving alleged violations of those expectations, and the rights and responsibilities of students and faculty members throughout the process.
  Students from other institutions will also be held to the same standards of the Rice Honor Code.
• STUDENTS WITH DISABILITY: If you have a documented disability or other condition that may affect academic performance you should: 1) make sure this documentation is on file with Disability Support Services (Allen Center, Room 111 / adarice@rice.edu / x5841) to determine the accommodations you need; and 2) talk with me to discuss your accommodation needs.

Course Material