CS438/591 Assignments

Homework 1

Due on Friday, Feb. 3th: Please do problem 2.1 to 2.5 (at the end of chapter 2 of textbook).. Submit by email attachment to TA at dabin@siu.edu or to the instructor by bring to classroom. For your convenience, you may download the problems from here .

Reference solutions to Homework 1

Homework 2

Due on Friday Feb. 24th, 4:30 P.M.: Please do problem 4.1 to 4.4 (at the end of chapter 4 of textbook) and submit by email to TA at dabin@siu.edu or bringing to instructor at class. For your convenience, you may download the problems from here .

Reference solutions to Homework 2

Project 1 [Due on Feb. 29th, 4:30 P.M.]

Please implement the four alternative motif finding algorithms (which can all be found from released online slides): BruteForceMotifSearchAgain (text page 89), BranchAndBoundMotifSearch (page 92), BruteForceMedianSearch (page 67, you may want to adapt to use the developed tree-move operations), and BranchAndBoundMedianSearch (page 95). Thoroughly test your program, collect actual runtime of each (shall use the average time from, say, 10 consecutive runs) with varied parameters (such as motif length l from 1 to 10 for example, and sample nubmer t from 3 to 10 for example), plot the performance data, and give your analysis and explanations regarding the results (A simple way to check the correctness of you implementation is to see if they all produce the same results on the same set of input and parameters). CS majors regeisted for 591, please also implement the fifth algorithm -- spllitting the median string into the "prefix + suffix" for more progressively pruning the search space and improving the performance.

Submission instruction: submit your entire project via email sent to TA at dabin@siu.edu (wrap up all source files into a zip file). Alternatively, you may submit a CD. Below is a checklist that you must include in you submission pack:

A readme.txt file explaining the running environment and basic steps to compile and run your programs.
A Brief report (1 or 2 pages) including plotted performance results and your analysis on the results.
All source files of your implementation (you may use any implementation languate of your choice, including MatLab, etc.), including any auxiliary files necessary for the TA to test your programs.

Here is the test dataset you shall use for this project.

Homework 3

Due on Tuesday March 5th, 4:30 P.M.: Please do chapter-end problems 5.9 and 5.16 and submit by email attachment to TA at dabin@siu.edu. For your convenience, you may extract the problems from here .

Reference solutions to Homework 3

Project 2 [Due on March 30th (Friday), 4:30 P.M.]

Given the following scoring matrix:

	A	C	G	T
A	2	-1	1	-1
C	-1	2	-1	1
G	1	-1	2	-1
T	-1	1	-1	2

and the test dataset , you are required to (1) implement the dynamic programming algorithm discussed in part 2 of chapter 6 for global sequence allignment (using a scoring scheme with the Affine penalties of which the gap opening penality is 0.8 and the extension penality is 0.3), and find out the most similar sequence(s) from given dataset for the first sequence; (2) modify your implementation (by incorperating the "free ride" idea) so that local allignments are uniformly performed as well, and then refind the most simmilar sequence(s) for the first sequence.

Note: You must submit all source files (to TA by email at dabin@siu.edu), including a readme file with enough details for TA to test your program, and a brief report mentioning the closest sequences you've found in both cases associated with the hiest scores, and any other interesting issues you found/experienced. Late submission is not accepted (or must be preapproved by the instructor if you have special diffculty).

Homework 4

Due on Wednesday April 11th, 4:30 P.M.: Please do chapter-end problems 6.5, 6.17 and 6.19 and submit by email attachment to TA at dabin@siu.edu (or hand in to TA in person). For your convenience, you may extract the problems from here .

Solutions to HW 4

Homework 5 (the last one!)

Due on Friday April 20th, 4:30 P.M.: Please do chapter-end problems 7.2, 7.3 and 7.8 and submit by email attachment to TA at dabin@siu.edu. For your convenience, you may extract the problems from here .