BMI 214
Spring 2007
Programming Project 1 Quiz

														Your name:
														SUNet ID:


Instructions:
-----------------
Some questions involve running your program on the provided input files 
(see http://www-helix.stanford.edu/bmi214/project1/alignments/for_quiz) 
and reporting the maximum alignment score; others are short answer.  

Do not forget to include the results of this quiz in your submission.  
Specifically, include a folder called alignments with inputs/outputs, and include your answers to the below problems.  
See the submission instructions in the main Project 1 handout for complete details.

REMEMBER that you must strictly follow the instructions for naming output folders and files!!!


Question 1: Global alignment of two DNA sequences.
Input file: alignment1.input
Alignment Score:



Question 2: Global alignment of the same two DNA sequences with different gap penalties.
Input file: alignment2.input:  create this file yourself by modifying alignment1.input gap penalty to (1.5 0.5 1.5 0.5).
Alignment Score:



Question 3  
Based on the output from alignment2, what is the last (right end) aligned subsequence (a region aligned between gaps) 
in sequence 1 (first sequence)? 
That is, what is the subsequence of sequence1 that follows a gap, that is at the rightmost end of the alignment?



Question 4: Global alignment of two protein sequences with gap penalty (1 0 1 0).  
Input file: alignment3.input
Alignment Score:



Question 5  
Based on the output from alignment3, what is the average number of gap characters in the first sequence?  
(The first sequence is the one that was on line 1 of the input file.)


Question 6: Global alignment of the same two protein sequences with different gap penalties.  
Input file: alignment4.input:  create this file yourself by modifying alignment3.input gap penalty to (1.5 0.5 1.5 0.5)
Alignment Score:



Question 7   
Based on the output from alignment4, what is the average number of gap characters in the first sequence?  
(The first sequence is the one that was on line 1 of the input file.)



Question 8: Global alignment of the same two protein sequences with different gap penalties.  
Input file: alignment5.input:  create this file yourself by modifying alignment3.input gap penalty to (4.5 1.5 4.5 1.5)
Alignment Score:



Question 9  
Based on the output from alignment5, what is the average number of gap characters in the first sequence?  
(The first sequence is the one that was on line 1 of the input file.)



Question 10: Local alignment of two protein sequences with gap penalty (3 1 3 1).  
Input file:  alignment6.input
Alignment Score:



Question 11  
Based on alignment6, the first aligned letter in sequence 1 is ?
(Clarification: If our alignment is
	HLEGV
	-KNWA	then the first aligned letter in sequence 1 is L)


Question 12  
Based on alignment6, the last aligned letter in sequence 1 is


Question 13  
Based on alignment6, the first aligned letter in sequence 2 is


Question 14  
Based on alignment6, the last aligned letter in sequence 2 is


Question 15: Local alignment of the same two protein sequences with different gap penalties.  
Input file: alignment7.input:  create this file yourself by modifying alignment6.input gap penalty to (5 1 5 1)
Alignment Score:



Question 16: Local alignment of two DNA sequences.  
Input file: alignment8.input
Alignment Score:



Question 17: Local alignment of the above (DNA translated into protein) sequences.  
Input file: alignment9.input
Alignment Score:



Question 18: Global alignment of the above (DNA translated into protein) sequences.  
Input file: alignment10.input:  create this file yourself by modifying alignment9.input to global alignment
Alignment Score:



Question 19 
Compare alignments 9 and 10. Which gives you a higher alignment score Ð local or global alignment?


Question 20  
Briefly discuss when you want to use local alignment.



Question 21  
Briefly discuss when you want to use global alignment.



Question 22  
Compare alignments 3, 4, 5 or alignments 6, 7.
When you increase the gap penalty, what is the general trend of your score change; increase, decrease, or no change?


Question 23  
When you increase the gap penalty, what is the general trend of the number of gaps in the alignment; increase, decrease, or no change?


Question 24  
Compare alignments 8 and 9.
Briefly discuss the advantage of DNA alignments (as opposed to protein alignments).


Question 25  
Briefly discuss the advantage of protein alignments (as opposed to DNA alignments).