CPSC536a - Assignment 1 (covers Modules 1+2)

handed out Wed, 02/01/30; due Wed, 02/02/06

1 DNA, RNA, Proteins [5 marks]

Consider the following (incomplete) prokaryotic mRNA sequence

guccaggagcag...gacucagacuga

(a) What is the corresponding complementary DNA sequence? [1 mark]

(b) What is the amino-acid sequence of the corresponding gene product (protein)? [2 marks]

(c) If the mRNA sequence were eukaryotic instead of prokaryotic, what could you say about the corresponding gene (DNA sequence) from which it was transcribed? [2 marks]

2 Genetic Code [7 marks]

As a reading assignment, you have read Douglas Hofstadter's article 'The Genetic Code - Arbitrary'.

(a) Briefly outline the thought experiment which is provided to support the hypothesis that the genetic code is arbitrary. (No more than 200 words.) [2 marks]

(b) Briefly outline the major objections to the hypothesis that the genetic code is arbitrary, as discussed in the article itself, including the postscriptum. (No more than 200 words.) [2 marks]

(c) Based on what you've learned so far, can you elaborate the objections from part b, lending them even more credibility? Can you think of additional objections to Hofstadter's hypothesis that are not mentioned in the article? (No more than 200 words.) [3 marks]

3 Local Alignment [6 marks]

Here is table resulting from a run of the local alignment algorithm (with linear gap penalty with d = -8) on the protein sequences ALSALS and ANAALL, using the BLOSUM50 substitution matrix:

	A	L	S	A	L	S
	0	0	0	0	0	0
A	5	0	1	5	0	1
N	0	1	1	0	1	1
A	5	0	2	6	0	2
A	5	3	1	?	4	1
L	0	?	2	0	12	4
L	0	5	7	?	5	9

(a) Complete the table, by replacing the "?"'s with the appropriate numbers. [3 marks]

(b) From the table, give the optimal local alignment for these two sequences. [3 marks]

4 Multiple Sequence Alignment [6 marks]

(a) Determine the sum-of-pairs scores for the following multiple protein sequence alignment, using the BLOSUM50 matrix and linear gap penalties with d = -8. [3 marks]

PAWH
PT-I
PA--

(b) Align the following two alignments of DNA sequences. Use the scoring matrix in which a match gets a value of +2, a mismatch gets a value of -1, and a (base,gap) pair gets a value of -4. A (gap,gap) pair gets a value of 0. [3 marks]

Profile 1:
ACGC
A-GC

Profile 2:
ACCT
ACC-

General remarks:

While cooperation between students - especially between CS and non-CS students - is encouraged, each student is expected to work out the actual solutions to the problems individually and hand in their own assignment. In other words: help each other, but do not copy solutions.
Feel always free to contact Anne or Holger if you feel you need further help than can be provided by your fellow students.
The assignment has to be handed in on the date it is due before or at the beginning of class.
This assignment should take you about 1.5-3 hours of work, if you have good knowledge of the topics covered and did all reading assignments. However, don't wait until the last minute relying on this estimate - it might not apply to you (or anyone at all), you might need additional time to consult the literature, ...