CS566 Fall 2006
Term Project
Project topics: You may select any of the topics listed below. You may also suggest your
own topic, subject to approval by the instructor. In either case, the project topic must be
finalized by beginning of class on Nov 1st.
Project teams: Up to 3 students may form a project team.
Project submission: The code files should include the names of the team members in the
form of comments at the beginning of each file. In addition to the code, the submission
should include a report written in the form of a research paper based on the template of
the journal Bioinformatics. At a minimum, the following aspects should be addressed.
Why did you do it?
Motivation or Significance
What did you do?
Objectives or Goals
How did you do it?
Design, algorithm and implementation. You may adapt pre-existing
code/programs. If you do so, you MUST clearly indicate what functionality you have
added or modified.
What did you find?
Results, validation. Analyze real world data using your program. Do the results
make sense?
Which are the other methods to address the same problem?
Comparison with other approaches. How is your program different or similar to
other existing resources?
Discuss your learning experience in the project
What was easy? What was hard? How would you extend your project? If you had
to do it again, what would you do differently?
References
Be sure to cite papers, web resources or programs that your work draws upon at
appropriate places in the text.
Part I of the project consisting of the Motivation, Objectives, Design, Algorithm
(including pseudocode) and plan for Validation should be submitted in hard copy by the
beginning of class on Nov 15th.
The entire revised project (including code and instructions to run program) should be
submitted in electronic format (either as a CD or by e-mail) by beginning of class on Dec
4th.
Project presentation: All groups should be prepared to give a 15 minute presentation of
their project in one of the student labs or the instructor’s office on Tuesday, Dec 5th
between 9:15 and 4:00 pm. You will need to schedule your time slot by contacting the
instructor via e-mail.
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CS566 Fall 2006
Term Project
Project Topics:
A. Genetic algorithm to align a pair of sequences. This is a simpler version of using a
genetic algorithm for multiple sequence alignment (see class notes/textbook).
B. Calculate similarity between two proteomes.
C. Pair-wise alignment of two RNA sequences. Take into account sequence as well
as plausible secondary structure in your approach.
D. 3D dot-matrix visualizer.
E. Modified version of the Nussinov algorithm that has a more complex cost model.
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