CBB752/CPSC452/CPSC752/MBB452/MBB752/MCDB452/MCDB752
http://www.gersteinlab.org/courses/452/Please select from the appropriate section and read the general note at the end of the page. Final projects are due by 5 PM on Friday, May 8.Please E-mail final projects to cbb752(at)gersteinlab.org.
MBB452/752 and MCDB452/752:
Pick one of the topics below and write a research paper. Research papers should be approximately ten pages in length (double spaced). Carefully cite your references at the end of the paper (not included in the 10 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).
CHOOSE ONE:
* 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?
* Synteny mapping seeks an alignment of entire chromosomes or genomes across species. Write a research proposal focused on the problems of creating these maps. What differentiates the creation of syntenic alignments from other sequence alignment algorithms, such as Needleman-Wunsch or FASTA? What technique would you use to create a synteny map between two species?
CPSC752 and CBB752:
Using the language of your choice, please select one of the following options. 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 (include the language version you used). A test-run showing the output put from your program along with your training/test data must also be included. Programs that do not run will not receive credit.
A significant portion of each program should be implemented from scratch and not simply rely upon calling existing libraries or packages!
CHOOSE ONE:
* Implement a multiple sequence alignment algorithm.
* Implement a simple structural alignment algorithm.
* Implement a simple sequence assembly algorithm.
NOTE TO ALL:
If you have another topic that you would like to write about or implement, please talk with Mark Gerstein and the TAs before Wednesday, April 22.