• Course Description
• Timing & Location
• Instructors & TFs
• Outline of Topics
• Lecture Summaries
• Discussion Sections
• Final Project
• Class Requirements
• Previous Years' Pages
• Research Opportunities

Final project

Pick one of the topics below and write a research proposal or implement a bioinformatics algorithm.

Topics

• Multiple sequence alignments cannot be efficiently handled using purely dynamic programming.  Write a research proposal dealing with these alignments.  How do existing methods approach this problem?  Can other information be determined from these alignments (i.e. phylogenetic trees or motif finding)?  What technique would you use to align a family of sequences?  Why did you choose this method over the others?
• As covered in class, structural alignments are less straightforward than sequence alignments. Write a research proposal dealing with aligning the structures of two macromolecules. Assuming that both structures are known, what issues arise in creating the alignment? Is it possible to produce a verifiably "best" alignment? What technique would you use to align two macromolecules? Why did you choose this method over the others?
• Implement a multiple sequence alignment algorithm.
• Implement a simple structural alignment algorithm.
• Implement GOR IV or a GOR-like algorithm.  You should include both a training and a prediction program.
• If you have another topic that you would like to write about or implement, please talk with Mark Gerstein and the TA's before Wednesday, April 30.

Additional Notes

Research proposals should be approximately eight pages in length (double spaced). Carefully cite your references at the end of the paper (not included in the 8 pages).  Please note that the papers are research proposals and therefore should contain both a) a review of the literature and b) a proposal for something new or an analysis of existing programs.  (i.e. Propose a simple project for a new algorithm or improving an existing algorithm, or select an algorithm that you feel best fits a particular research task and explain why you selected that algorithm.)

If writing a program, please submit source code and a brief (one to three pages) write-up explaining: the task your program is used for, the algorithm you implemented, and instructions for compiling and using the program.

Due Date

All projects must be submitted on or before Wednesday, May 7 by 9 AM on Monday, May 12.  Please submit an electronic version of your project on the Classes2 server (http://classes2.yale.edu).  No hard copy needs to be turned in. Your project will be put on our public website after grading (http://www.gersteinlab.org/courses/452/).